Here are some technical answers, sorry for the delay !
Does it allow collaborative editing of graphs by users at the same time?
Collaborative editing is possible, since the same data can be edited by different users. However if you are talking about google-doc-like real-time editing, we do not see key advantages to that. It would be a lot of work, and many challenges would probably arise.
Does it allow direct and indirect LDP containers?
For now it handles only direct containers. We will probably handle indirect containers in the future.
I see you are making opiniated choices in SemApps, like dependency on WebID module, where imho you should take care not to have them become fixed requirements for users of SemApps, i.e. make alternatives easily re-configurable with minimal coding.
I don’t think there is a dependency to WebID, but if we did add that by mistake, it is certainly possible to remove it. The WebID of the logged user can be added to SPARQL requests in order to handle ACLs (not implemented yet on Fuseki-side), but if no WebID is provided, then Fuseki will assume the user is anonymous.
SemApps instances will interoperate seamlessly, but other platform interop depends on the individual interpretation of their developers of said standards and ontologies. This is where the Fediverse is at the moment: lotsa production-ready apps, but a hard road to seamless federation between them. Standardizing here now has a lot of catching up to do.
Yes I agree that this is a major challenges. We hope we will find common spaces to discuss the issues that arise as we try to make our apps interoperable. Very happy to see your enthousiasm @aschrijver, and looking forward to future collaborations !