Fantastic post.
You have jumped really far in a short amount of time. Very impressive. Lets hit your questions. right off the top.
QUESTION ONE
What I have personally observed is that at the origin and insertion points of muscles - the overlaps are simply softer. The shapes are there, the volumes are there, but how do we represent 'Less Anatomy" so that it doesn't look like a ecorche model. If you wanted it to look more like it, it would be almost no body fat or flesh.
We have to step away from the mannequin quick sketches and try to stylize the drawing on top with some surface anatomy. More experience with anatomy knowledge will let you do this sooner with your gesture phase, and spend less time in your structure phase. That is if we are thinking about it in this sort of order.
1.Gesture,
2.Structure,
3.Stylize.
The last one of course would end up to be the style guide for something like a Riot game vs.....Pixel art. it becomes how you represent form vs shape. and an overall style.
Surface anatomy/Skin Anatomy/Flesh...anatomy? (last one sounds funny)
You know...the giant organ of skin that cools you and grows hair on top of fat deposits....outside of the muscles.
That organ and fat --- will really do a lot designing - when we regard people as a "type" - a body type that is. Imagine the trope line ups of different body sizes of athletes of different sports.
But what if they are not that different and are just "Normal" shaped people (no body shaming - Just talking...NOT a super hero with an 8 pack) - Think subtle-just like the difference between two healthy adults one who just gets a average exercise regimen, and one who just lives healthy with no focus on exercise.
One will just look softer. One will have more definition between the muscle groups - but they are still soft transitions.
Line art is hard to do that with.
1. inside the overall shape - the line art is lighter, softer - or implied (see example notes)
2. outside the overall shape of the torso is thicker lined- to reinforce the idea that "everything is a shape". it makes the "subject"-whatever it is, stand out.
Generally with line art - weather its pencil or ink - Overlaps of big shapes like limbs
(which is rare unless contortion happens )-
or clothing - in front of one another
(or clothing sections in character art)
are thicker.
Lastly - occlusion shadows are also emphasized to be a bit thicker, to emphasize elements overlapping. And they only occur....near overlapping elements and shapes.
You don’t have to do perfect line art before you paint- just good sketches. Line art takes time and is a nice presentable drawing and an asset you can paint later. If you want to paint you just need clear and understandable line art.
QUESTION TWO
I guess my answer is kind of redundant - but the overlaps and the shapes of the feminine muscles are VERY subtle, and MUCH softer than that of the masculine ones. Animation styles will have much less anatomical information and have more essence of the shapes than of the forms.
Female models tend to have more fat deposits in some areas, and also the top of the femurs are represented wider than the tops of the humerous when shape is concerend.
Or a narrower waist that SEEMS taller but the oblique doesn't have the mass a male version does, so the line from the bottom of the rib cage can swoop down all the way to the great trochanter.
When you find some ref for style examples, (art parents, art gods...whatever) find which areas are thicker and thinner where they emphasize shape and overlap forms. You'll have to derive your style choices based on personal preference. Or go nuts and make a sketchbook like Da-vinci discovering all these things on your own.
Anime is one extreme that can push that idea to make you think - oh wow - this really is all made up shapes and skewed anatomy.
THOUGHTS
Welcome home brother...welcome home.
20 Iterations off the finite curve there's a young artist that works more with simple shapes than youtube paywalled mystified bullshit.
But he's no dummy..
He realized what reality was...and wasn't.
He read an article from a master.
So he shaped reality too his own whims and desires one concept at a time.
We take that enlightened perspective and put it on a loop in his mind......
And the chemical his brain excretes we put in every bite...
....of Simple's Shapes Simple Wafer, Wafer shaped Cookie.
Come home to the taste of shattering the grand Illusion.
Come home...to simple shapes.
THOUGHTS 2
Just take your time. Zoom in if you have too.
Try an airbrush, soft edge simple round first. Identify the shadow into sections.
- Is it on the light side or the dark side of the generalized shadow/light separation.
- Shadow side -terminator, cast shadow, bounce light, ambient light, and occlusion
- Light side - local color, mid tone (or half tone), and highlight
Howard Pyle, a great instructor - Says to put your information in the light or in the shadow for the overall composition.
What that means is if your dark side is blacked out like your reference - the light side has all the 'information' Look at all those middle tones turning the form. But they dont get as dark as the shadow shape.
Parahrasing - "The darkest value in the light, should never be as dark - as the lightest value in the shadow. "
He also says you only need 4 (two for each side of the separation of light and dark side) for the focal point. Maybe 5 for details. Any more and it becomes a trivial mess of information. Everything else you could get away with three.
Shadow Shape - is it form shadow, or cast shadow, or affected by bounce light? Or terminator shadow?
Light Side - is it half tone turning away from the light? Is it a specularity highlight?
Where these...shapes...of shadows transition into one another - is it soft because of the form - or a hard cast shadow by some form sticking out.....
Now how do your references form the art that you consume look? Information in the light, or shadow - two values in the shadow- and three in the light? Three values in the shadow and two in the light? Maybe a highlight dotted on? All preference to the artist. ---And also the draftsman solving the problem of where to make the eyepath go.
THOUGHTS 3
I'm gon' tell ye' raaaaht' nooooooow..................you are going to be great--
Just do what you said here. Find the answers to your own questions. Reach out, but dont wait for other people to answer. You just need words to search for sometimes. -- If you want to help others - its just Drawing - Values - Edges - Colors. Those are the fundamentals of picture making. Pick one and help them with it.
I re read that last quote that and realized I touched on it where you get into your own studies of your "art parents" or "art gods". You have to see how others solve problems. Smart moves. You were already on the right track. Just do what you felt there.
Be your own worst critic people always say --- What that means is just write down the questions and go search for the answers.
People just write down the questions here, then I answer them with information I learned myself - or from school or a youtube video if I dont know the answer. But I knew the words to search for that's the only difference.
Get - Devin Korwin's "Advanced Basics" organize your fundamentals into digestible steps for picture making. And Clint Cearly's pdf's on color, composition and mood so you can break down the ideas into digestible steps for picture making in a book form - and not scrub videos or wait on a critique that might forget to include something. 
The last thing I reccomend is to just hit the books and learn some artist anatomy for shapes of muscles from different people - what bones they attach to and where they start and end (origin insertion). Hampton, TenTen, Bridgman, ModerndayJames, Proko - WHO CARES because what you have to do is draw your own drawings to put the shapes in your mind. This is the only thing that is not about making nice drawings and - and more like doing pullups or running on a treadmill.
Now Lets go draw B!
