I've always had a similar situation in trying to merge the Stirk Compatibility patch into TR_Stirk itself (can't stand a whole mod slot going to just the removal of a boat!). However, when I do the merge, and then in bash switch the master (as it would then rely on itself) to another esm, nothing would happen, the boat would still be in Anvil.
So with what you said above, if I convert TR_Stirk to a master, use merge to master to incorporate the compatibility patch, and then convert the now completed merged esm back to an esp, will this work?