Ok, I'm kinda behind the times here, so pardon my ignorance, but huh?
What even is Pokemon Transporter?
I'm just talking about placing a pokemon directly into the box (Bill's PC) no trading or anything.
I use PKHeX to pretend I caught ideal pokemon. I catch a Pokemon in the game, then use PKHeX to make one with the same met location, ball I used, date, etc. So, if I catch a Misdreavus in Cliff Cave, I don't see how it would end up with Pokemon Transporter as it's met location. It would just have Cliff Cave, where it was caught.
Does this make sense, or am I just being more confusing? In a nutshell, I don't use PKHeX to give myself god tier hacked creatures. I play through the game legitimately, and when I catch a favorite pokemon of mine I make an "ideal" replacement and replace the one I caught legitimately with the ideal one. Then I train it up as usual.