At worst, it makes it somewhat more awkward to fuse in
another setting if that ever comes up, but there's a lot of room in such an unexplored world as the Works home reality; they're literally isolated in a pocket reality in a corner of Japan and never talk about current events in their world.
Many Nasuverse stories exist in a isolated bubble within the larger setting and could coincide, unless they explicitly change the larger setting as part of their premise (Apocrypha, Prisma Illya, etc) and
even those could coincide with things that aren't
Fate.