TVH doesn't actually ID muxes by TSID (yet, though this will change). However I don't think it will accept the same service TSID/SID combo, so if the service IDs are duplicated on muxes reporting as TSID 0x0 then yes I can imagine you will have problems.
You could manually edit the config files to assign muxids to the muxes, however I think that might get auto overwritten by TVH AND I think generally TVH will get upset as while it doesn't use TSID for the unique ID I think it still expects this to match the incoming data in several places.
SO basically yes I think short of bodging the code completely you're a bit stuffed :(
Adam