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Can't you get the same result by adding "Advanced submodules behaviours" and then selecting the "Recursively update submodules" checkbox?
If your $BRANCH argument is something other than master, then you'll need to set "Branches to build" to the value of $BRANCH.
While I agree that the item you list as #2 is correct (branch section is not written to .git/config file at clone), I don't understand its relevance to your use case. Are you dependent on the contents of the branch section of the config file for something special in your build process, or just noting a difference which you detected, but which is not relevant to your actual use?