Mark Trainer.run_stage as protected

[awaelchli]

What does this PR do?

Follow up to #10896
Part of #10987
Parto of #7740

Trainer.run_stage was previously public and accessed in the dispatch methods of the TTP. After #10896 it remains a Trainer exclusive method.

Before submitting

• Was this discussed/approved via a GitHub issue? (not for typos and docs)
• Did you read the contributor guideline, Pull Request section?
• Did you make sure your PR does only one thing, instead of bundling different changes together?
• Did you make sure to update the documentation with your changes? (if necessary)
• Did you write any new necessary tests? (not for typos and docs)
• Did you verify new and existing tests pass locally with your changes?
• Did you update the CHANGELOG? (not for typos, docs, test updates, or internal minor changes/refactorings)

PR review

Anyone in the community is free to review the PR once the tests have passed.
Before you start reviewing make sure you have read Review guidelines. In short, see the following bullet-list:

• Is this pull request ready for review? (if not, please submit in draft mode)
• Check that all items from Before submitting are resolved
• Make sure the title is self-explanatory and the description concisely explains the PR
• Add labels and milestones (and optionally projects) to the PR so it can be classified

Did you have fun?

I made sure I had fun coding 🙃

Part of #1 (it's a lie, this is just here to avoid noisy GitHub bot)

cc @Borda @tchaton

[tchaton]

LGTM !