Fix 'Would you like to clone the submodules?' prompt under msys

[zvecr]

Description

When running qmk setup on msys, with missing submodules, the "Would you like to clone the submodules? [Y/n]" prompt refuses to accept any input.

Questions asked before the check_binary_versions call work, anything afterwards, broken.

From https://github.com/clueboard/milc/blob/master/milc/milc.py#L170-L173

        # On some windows platforms (msys2, possibly others) you have to
        # execute the command through a subshell. As well, after execution
        # stdin is broken so things like milc.questions no longer work.

Types of Changes

• Core
• Bugfix
• New feature
• Enhancement/optimization
• Keyboard (addition or update)
• Keymap/layout (addition or update)
• Documentation

Issues Fixed or Closed by This PR

• https://discord.com/channels/440868230475677696/473506116718952450/1344341968930476063

Checklist

• My code follows the code style of this project: C, Python
• I have read the PR Checklist document and have made the appropriate changes.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• I have tested the changes and verified that they work and don't break anything (as well as I can manage).