Yep, the higher the AIP, the more of the wave will be MkII instead of MkI, until the AI hits Tech Level II and the waves are 100% MkII, then it'll start mixing in MkIII ships. This was added a while back to smooth the transition between tech levels; in theory it makes the game harder, but in practice you get a much better feel for how your defenses are doing, and aren't blindsided by a sudden jump to higher mark waves. Looks like this was added waaaaaaaaaaaaay back in 5.036, and we're on 7.043 now.
The new HW defense exos are pretty new (about a month old). As I understand it, they're supposed to get harder, but they stop if you kill that AI Home Command Station (this will cancel the currently-charging exo). Once you start a homeworld assault, you either need to finish it or it will finish you.