This is one that would be good to rewrite to extend filestorage, in fact I've done that experimentally but don't seem to have kept it .... extending a package takes care of the copying of parameters, calling of instantiate, etc that ajax-file-storage does (in fact it's very close to manually implementing the package extends concept).
So if I understand, that would that enable it to play nicely with Layout-Manager?
As an aside, I note that when the File-Storage includelet appears in the site-map it is named 'Documents' even though in my case the original File-Storage module is mounted with the name 'File-Storage'. Of course it can easily be renamed but the other includelets have matching names. Was that something I did or is it hard-coded somewhere?