but when the dependencies are installed, the git creds are not taken in account

I have to admit, we missed that use case 😞
A quick fix will be to use git ssh, which is system wide.

but I want know to switch to git auth using Personal Access Token for security reasons)

Smart move 😉

As for the git repo credentials, we can always add them, when you are using user/pass. I guess that would be the behavior you are expecting, unless the domain is different... Maybe a flag to turn it off, if you want?!