i saw there's an auto-focus setting, and it works well. but once selected, i cannot unselect the text box on the Crafting Terminal
preventing me from pressing R or U to use JEI until I reopen

I +1 this and can consistently reproduce this, it has aggravated me quite so.

I'd like to also add, even if you have the auto-focus option off, upon selecting the search bar there is absolutely no way to deselect the search bar, even if you select the JEI search and deselect it, the ae2 search is still selected.

Good morning,
I see that this was closed as I assume "won't fix"?
I wanted to display my displeasure with this, I understand your reasoning behind this, but I'd like to argue that the benefit of UX far outweighs the consistency in this specific situation, I would appreciate a second visit on this issue.
P.S. this issue is not present on the "All The Mods 8" modpack, I'm not sure how, but it behaves exactly as expected.
P.P.S. If I have made a fundamental misunderstanding please inform me.
Nevermind I'm a total idiot who doesn't read before I speak.

i saw there's an auto-focus setting, and it works well. but once selected, i cannot unselect the text box on the Crafting Terminal
preventing me from pressing R or U to use JEI until I reopen

This really seems to be intended Vanilla behavior now 🤔
There's just nothing in Vanilla that actually unfocuses if you click on an unfocusable element.