This bug makes it impossible to use gpg-agent as ssh-agent for keys generated from gnupg.
(How should I understand what passphrase should I enter?)
The only way is to load them with ssh-add.

Could you say, on which platforms exactly it should work?

Yes, due it uses adwaita-qt theme.
Yes, I can start it on the command line and it works, but gives a warning.

It's white due to https://dev.gnupg.org/T4144

Moreover, pinentry-qt doesn't ignore env if it runned from gpg-agent. So you are wrong about technical reason.

for comparison pinentry-qt doesn't ignore env:

"partially" means it doesn't allow to input elsewhere, but in case of focus loose input will go nowhere

At least it MUST NOT grub input with no-grab option. But it doesn't allow to input elsewhere in any case.

I don't know about gpg-agent, but pinentry-gnome3 ignores $GTK_THEME (and $GDK_SCALE) even if I run it directly:

$GTK_THEME=Adwaita:dark GDK_SCALE=2 /usr/bin/pinentry-gnome3
OK Pleased to meet you
GETPIN

It's possibe to do via gtk3 directly:
https://developer.gnome.org/gtk3/stable/gtk3-General.html#gtk-device-grab-add

By grabbing I mean that it's not possible to input elsewhere. Same as ssh-askpass does.

By grabbing I mean that it's not possible to input elsewhere. Same as ssh-askpass does.

I confirm this bug!