Running ./boot creates/modifies config.sub files, resulting in dirty git tree

As of !5057 (merged), if I run the ./boot script in a clean checkout of GHC, it dirties the git tree thusly:

$ git status
On branch master
Your branch is up to date with 'origin/master'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
  (commit or discard the untracked or modified content in submodules)
        modified:   libraries/unix (modified content)

Untracked files:
  (use "git add <file>..." to include in what will be committed)
        libraries/base/config.sub
        libraries/ghc-bignum/config.sub

no changes added to commit (use "git add" and/or "git commit -a")

In other words, ./boot creates two config.sub files that aren't checked into version control and modifies another config.sub file that is checked into version control.

What should be done here? I don't think we can just add config.sub to .gitignore, as several submodules (e.g., unix) already check it in. cc @angerman