When IndependentBranches is turned on, library filter on 'Patrons' menu page ('cgi-bin/koha/members/members-home.pl') only allows the current user site. In spite of the use of the 'view_borrower_infos_from_any_libraries permission', it's not possible to search for patrons from other libraries, even if we're part of the same group of libraries. We can access patron account using the url. No modifications are allowed whether we set IndependentBranchesPatronModifications to 'yes' or 'no'. See also Bug 12599 - IndependentBranches Holes
Yes, I think we could replace some of our features with the new "library group" mechanism. IndependentBranchesPatronModifications, IndependentBranches, "Branches limitations" for patron's categories and AV, etc. Not trivial however.
IndependentBranchesPatronModifications is just for moderating patron address change requests. I think the library group feature and the Independentbranches are incompatible. Or to say it differently: the Independentbranches is stronger and 'overwrites' the library group feature. I feel like for now this is intended until we have fully replaced all features of Indepdendentbranches by library groups (and can then also remove the feature itself).