Which is inevitable, really, given that the parser function adds links to the templatelinks table to ensure cache integrity. Nonetheless, they're *not* templates, they're *not* transcluded, and they *shouldn't* appear below the edit window.
I have a nasty feeling that this is not solvable without a complete overhaul of the way functions like this and #ifexist: handle cache coherence, or at least an extra field to allow these additions to be marked as 'silent' or some such. Both will probably require a schema change; marking as such.
Related: bug15735, bug12019 - same issue for #ifexist: