If there is a two-way transitive trust between the two domains I don't see what the big deal is (certainly, Multistore is overkill for this application).
The filer will act like any other Windows server with regard to domain SID resolution. Pick a domain to host the filer, and use AD global groups & local groups to map users to resources across the trust as needed.
The cifs.search_domain option is only useful for prioritizing the domain search order. If you leave it blank it will search all trusted domains for mapping usernames. With only two domains this is not necessary.