I don't think base-uri(.) and $base are necessarily the same, nothing really prevents us to add "out of base" resources to a file set in some tweaked use case, so I'd be more confortable with using base-uri(.), which is correct 100% of the case.

I don't think that particular point would be a performance issue (since the XPath processor has direct access to the node's base URI as part of the XDM).

Interesting about the performance issues though. Do you know what's the bottleneck ?