Typo? In any case, avoid the weird debug-level setting. Use "debug ipc"
instead. Also set log-file so that the logs don't end up in some random place
(or nowhere).
Yes typo. I removed it alltogether for now:

pinentry-program /usr/bin/pinentry-qt
enable-ssh-support
ttyname $GPG_TTY
default-cache-ttl 60
max-cache-ttl 120

Very likely gpg-agent fails to start pinentry-qt or pinentry-qt fails to start
because there's no window manager running. Try using pinentry-curses or
pinentry-tty instead of pinentry-qt if you are anyway using the terminal.
In fact gpg-agent seems to be able to call pinentry-qt, as when I use pass or browserpass, it works and I get a pretty pinentry window...

That said, switching to pinentry-tty does not solve the problem with pam.
In fact I can see pinentry-tty working with pass and failing with sudo in the same terminal session:

$ pass perso/ameli.fr
Please unlock the card
Number: 10 955 601
Holder: Franck Routier
PIN:
*************************
$ sudo su
Insert authentication card for user `franck'
Trying authentication as user `franck'...
[sudo] password for franck:


Franck
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