I know there may be some different opinions on a throttle body spacer. However I will give it a try and test it out versus just assuming what it can and will do without actually having one or a prius to test it with. This is a 12mm spacer and I will be installing it once I get my latest purchase. A Big Bore Throttle Body
^ The circled bit, which connects to the air filter box, will move up 12mm; not sure of the ramifications, singificant or not. That aside, I googled, and the consensus was if it does anything it's pretty darn subtle.
I do not have the stock air filter. I am using a Blitz warm air intake. This sits lower than the stock intake. All should be good with the TB spacer. Your concern is valid to those who use a stock intake though and thank you for your input.