The GUI for signal requests shows green checkmark "apply" button, but pressing E (hotkey to press the green button) closes the GUI instead.

What version of the mod are you using? The green "confirm" checkmark hasn't had (E) as part of the tool tip since version 1.14. That was fixed in 2.0 and beyond.

Screenshot: https://disk.yandex.ru/i/IF_lDmmQBsrYGw
Mod version: 2.0.6

For those signals you must click the green check-mark to confirm the change. The 'E' is the Close UI in this context.

For those signals you must click the green check-mark to confirm the change. The 'E' is the Close UI in this context.

Yes, that's what I'm telling.
The Factorio help tates that E stands for the green button.
Screenshot: https://disk.yandex.ru/i/MTrCWuZA1Fke-Q

The behaviour was changed in the Release 1.1.0:

the Close GUI key-binding (default value is "E") was renamed to Confirm Gui. It works the same as before for many cases (just closing the GUI), but in a lot of other cases, it works as confirm, which generally means the same as clicking the "green button".

I'd consider this maybe a UX improvement, but lower priority at the moment.