This is an interesting question. In the publication properties there is the option on the snapshot tab to run extra scripts before and after the snapshot is applied. This is the same for both merge and transactional publications (below).
Many DBAs will have scripts which drop all the FKs on the subscriber and readd them after the snapshot is applied so the initialization runs smoothly and we don’t get the following sort of error:
“Could not drop object ‘dbo.tCity’ because it is referenced by a FOREIGN KEY constraint“.
However the snapshot generation is different between Transactional and Merge. In Transactional all the FKs are dropped for you and re-added later on. This doesn’t happen for merge. There’s probably a good reason for it but can’t see why they should run differently at present. Anyway, the message is that you don’t need to roll your own logic to deal with subscriber FKs in Transactional but you still do in merge!