You are correct that the resource manager will get different branch qualifiers for the same XA resource at the different servers - it will get the same branch qualifier at any single server (even during reentry), e.g. for node flow of 1,2,3,2 the bqual for the XA resource at 2 would be the same for both flows but it would be different at nodes 1 and 3).
OK, but that does mean that accesses to the resource manager from nodes 1 and 3 will be treated as a separate global transaction with respect to isolation - ie work done, and locks taken, at node 1 won't be seen at node 3 (search for loosely-coupled in the X/Open XA spec for where this is covered).
Since the remoting protocol is not demanded by the JTA spec, is it the case that the issue I raise is a non-issue?