> So does this count as a form of intelligent design

No, because the resulting organisms are still very much evolved rather than designed. They still have masses of junk DNA and stupid path-dependencies like the appendix and the recurrent laryngeal nerve.

> would a hypothetical alien race be able to detect this kind of intervention by examining future species?

Yes; we've been able to tell from its genome that brewers' yeast is an ancient deliberate hybridisation of two wild yeast strains, so future aliens could presumably do the same.