How to design ACL for a multi-level organisation
IMHO it seems like you really need a consultant for this stuff.  Hopefully an organization of your size (400 chapters with an unknown # of people per chatper) has budget for help.

But let me offer a few bits of advice: 


the "corresponded Organisation Group" as you put it CAN be a smart group, thus people (not admins) can self-select their own groups when they signup and/or register if you use a custom data field for "select your chapter".


CiviMember Roles Sync doesn't work as you describe, that's Civi Group Role Sync for that functionality
I'm not sure why you feel people need to use CiviGroup Role Sync
Don't understand your point 2.3



So I hope that helps, I've done this on a smaller scale for a group with 12 national chapters and 20-30 people per chapter, it works pretty well.  Please remember I do think a consultant with experience on ACL is needed.