I just set the git credentials in the

clearml.conf

and it works out of the box

git has issues with passing the user/token from the main repo to the submodules, hence my surprise that it is working out-of-the-box.
Do notice that if you are ussing ssh-key this is a none issue.

Nope, no

.netrc

defined anywhere, ...

If this is the case can you try to add the following to your "extra_vm_bash_script"
echo machine example.com > ~/.netrc && echo login MY_USERNAME >> ~/.netrc && echo password MY_PASSWORD >> ~/.netrc