I'll be the first to admit I am somewhat clueless where the internals of an auto are concerned, I prefer manuals, myself.
I'm not sure of all the ways air gets in, all I know is that when you hear that whine, it's usually because there's air in the system and it's not a good indicator.
The key is that in 99% of the installs I have done, the tranny NEVER whined and those that did whine, died 100% of the time.
Back the first time I recall hearing "that whine", many moons ago, it was because I got pissed and slammed the tranny into the converter and forced it together.
Later I found I'd cracked the pump housing and it sucked air in that way.
The car went a whole 10 miles.
Another way the pump housing gets cracked is if you DROP a tranny, like I see fools in self-serve yards do, straight from the engine to the ground, with the converter sitting on the input. :bang
During install I ALWAYS try to manually seat the tranny case to the block.
While doing so, I make sure the converter is spinning free, if it locks up before the case seats at least to the dowels, I take the tranny clear back out and make sure the converter is correctly engaged to the input and the pump drive slots.
Sometimes people think the converter is installed correctly and try to "draw" it up to the block with the bolts, then realize they need to finish seating the converter and many times it's already too late.
I've had trannies, especially ones with NEW converters, where you had to stand them on end to get the torque converter to fully engage the pump drive slots!
Pretty rare and unnerving.
Mark.