Great job! i had managed to fix this issue with your help.
for later readers, acng.conf exists in /etc/apt-cacher-ng/acng.conf.
so, first doing
qvm-run -u root <cachervmname> xterm , then
sudo vi /etc/apt-cacher-ng/acng.conf , then adding the
PassThroughPattern: ^dl\.flathub\.org:443$ in the arbitrary line without #, will make things work.
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