Generally speaking, the alternate abilities come through the 35K packs. I've had a heck of a time getting the alternate zombie abilities from any packs. I have all the plants abilities, but only have one alternate zombie ability, which I've had for a long time. I think I can safely say that you won't get them from the 40K packs, as I have bought millions worth of them in pursuit of the legendary characters, which search I recently finished.
Because I'm not concerned about collecting all the customizations, I have nothing left really to spend coins on but the 35K packs, outside of Rux and consumables, trying to collect the rest of the abilities. If I had to guess, I've recently bought around 20-30 amazing brainz packs along with the odd wondrous pack of greatness, and have yet to get one ability from them. Contrast that with my daughter's account, which I've recently earned a lot of coins on. I have her buy the plant 35K packs, and I'm watching her just rack up the plants alternate abilities!
You can console yourself with knowing that a large percentage of the player base considers very few of the alternate abilities to be better than their counterparts. One that I can think of is the iron maiden for cactus, I'm sure there are others, but I'm sleepy. Some are universally reviled, like the armored heal station for scientist.
