Poppy's ult should not cause invincibility on enemies.
There's not a good enough reason for it to cause invincibility on enemies.
If the reason is: "Well, the point of her ult is to knock enemies away. If it didn't make them invincible, then her knock-away could be interrupted by another form of team CC."
Then my response is that is also possible with other existing CC in the game. The point of blitzcrank's grab is to pull an enemy closer, but this can be interrupted by a Janna tornado, a Nami bubble, etc.
If the response is: "Well, that's only a normal ability, and this is an ultimate. It would be too detrimental to have her ultimate be nullified by a normal ability from your team."
Then my response is that that is also possible with other CC ults, including suppression ults. Malzahar can lock someone in place, and Alistar can headbutt them out of it with a normal ability.
If the reason to make the invincible is: "It would be messed up with Yasuo ult. He would go flying away with them all the way to the base!"
The my response is, no, Yasuo's ult stops the knockup/knockback and he finishes his ult off of it. Blitzcrank or Alistar can pull or headbutt, and Yasuo can immediately ult on those moves, effectively canceling the full length of the pull/headbutt.
If it's: "They're just doing something different."
Then my response is, why? How is making the enemies invincible interesting or fun? Why would I want a detrimental ability on my team when it's possible to have 5 champions with zero detrimental abilities on my team?
If it's: "Targeted dashes like Vi's ult, Maokai's twisted advance, or Lee Sin's Q would be weird, because they'd follow ALL the way!"
Okay, but that's kind of cool though. If you have to choose between Lee Sin accidentally Q'ing into their knocked-away team, and dying because of that, OR, Poppy making a high value target who is carrying their team and kicking your butts (such as Talon, Fiora, Riven) temporarily invincible with her mini-ult (just the knockup), which only causes YOUR nuke on that CC'd Talon/Fiora/Riven to do no damage, AND allows the Talon/Fiora/Riven enough time to regain all their cooldowns, and then kill you. Which seems more "Toxic"?
Also, which is more LIKELY to happen in normal gameplay? An alistar flanking the enemy team with intent to headbutt one into your team, meanwhile while the teammate Poppy is not on the same page whatsoever and wants to ult them all away. Alistar cancels one of the ulted enemies with his headbutt. OR! Poppy using the short range knockup and protecting an enemy while the rest of the team is trying to kill them. Which is more likely to happen in standard gameplay? I'd say the latter, which is a bad thing. The first situation is not any near as detrimental to the team.
I'd be fine with either of these options:
1.) Enemies should be both CC-able AND damageable while they are in the air - like every other knockup in the game. This means a hard interrupt COULD potentially disrupt their Poppy knockup. It's not very likely. 2.) Enemies are immune to CC in her knockup but can still take damage.