I really wish there was a way for us to gain the flying skill without using the astral tadpole.
There is. It's called the Grant Flight spell. Also, Draconic Sorcerers get flight as their level 11 subclass perk.
It would be really nice if you refused all tadpoles you get flying as a reward.
Someone's not been listening to the Emperor.
He talks about how he doesn't want to go back to being non-illithid because of the powers he has. He pushes onto you the Astral Tadpole because he knows that ceremorphosis brings valuable abilities, such as flight.
Refusing the tadpoles is specifically opting out of the powers that they provide. It would make 0 sense to opt out of all these increases in power and then suddenly manifest the ability of flight out of nowhere.
At best, they could have a situation that enhances your original tadpole like Ormeluum's probing or the Zaithisk to grant flight... But it kind of defeats the whole "Lure of power" aspect of tadpoles if you get one of the stronger abilities irregardless of if you give in to ceremorphosis or not.
I'd rather they just debug the AI so companions follow you across gaps better.