I feel like if you hit someone in the face with your atemi they will probably not be put back in balance, rather that can create a 'suki' or gap in their balance that can create an opportunity for nage to exploit and safely make their first movement. Granted we don't want to hit someone in the face so stoutly they move too much. When they, hopefully, block I like to drive my atemi into the block to start taking them off balance. I always atemi for the face/eyes because it obfuscates uke's vision and, when they block, you can drive your hand into their blocking hand...thus pushing his head/shoulder girdle area behind his hips. This is also why I always telegraph my atemi...which gets uke thinking about that atemi vice what you are really trying to play with.
But I agree that atemi can disrupt the flow of a technique if applied incorrectly, effectively putting uke back in balance. I feel like atemi is often overlooked in teaching and students just apply it a la 'monkey see monkey do' without understanding the how and why of its mechanics.
See my point is, if you are applying a kuzushi such that their heads are going BACK, then that's not appropriate for a technique where you need their weight to go forward, such as an ura/tenkan kotegaeshi.