In particular, I'm thinking of ghc-mod (but liquid might also be in this boat).

stack exec sets the binary path to include the snapshot's bin directory and the compiler's bin directory (where things like ghc and haddock can be found). There is currently no high-level way to add a binary to all projects using the same compiler version; you could manually copy the binary to the same directory as ghc, but this doesn't seem like an ideal solution.

These binaries are typically installed for a user but, once compiled, care only which ghc version compiled it, not the snapshot it was compiled with.