...Yeah...saw those Alpha planes in an earlier update of yours and thought man that was clever and will look cool. I think you need a twist modifier on them though.
I would guess, the character has been scaled non-uniformly without resetting the transformation matrix afterwards...try reset XForm before adding the Skin Modifier...
Editable poly and edit mesh have their own sub tab to set smoothing groups with. You don't need (and have no reason) to apply the modifier to work with smoothing groups.
I've never had much success with mirroring weights under the skin modifier. I'm probably doing something in the wrong order. Maybe I misread something in the tutorials.
anrent you doing the same? working on skin modifier-> *pose if it works -> delete the pose -> fix bugs ->* (there arent any muscles on fthe frontside of the foot, they're on the back)
Very unique way of doing it. I never thought of using lattice for it. I just duplicate it, apply a push modifier and then then wire material on top. Same effect, though.
yuo could addd an edit mrsh on top, do your editing, move the edit mesh below the skin modifier , then 'collapse to'. You should be left with skin intact.
I found this video pretty helpful for manipulating channel maps for game assets in Affinity. https://forum.affinity.serif.com/index.php?/topic/37474-how-do-i-modify-channels-freely/
So use the poly modifier to tri up the mesh, and then optimize it for whatever I'm doing, unless the models tris already look ok and don't cause a problem, like when its on the cap of a cylinder.