but I've gotten a couple weird pops, one in DRV when I trained JR
This is the standard pop that was there also before the cross training.
and one in Free Throws when I trained Pressure.
This, however, is not
It is annoying that the primaries are slower but if all of you guys have to deal with the same issues it can't hurt me (or anyone else) that much really.
That's true. If someone is training specialized outside or inside players, they can't be happy about this change. If they are training pure outside guard, they can't be happy their OD or PA training goes into RB, SB or ID, although ID is a good thing to have on guards. But if he doesn't want ID, that's his choice. Same with bigs; if you care just about 3-4 skills, you don't want 10% to go into JR or DR.
So managers who train multi-skill players are rewarded more, but it's a change so minimal that it matters only if you are training someone 1-position for 6+ seasons. Such players are usually NT caliber and they need multi-skill set anyway, so no harm done.