>would the tool also change master to the new merge commit
Not in my experience, no.
The goal is just to keep you aware of what problems you're likely to run into if you tried to push for your change to be merged in at the present moment. If these problems are due to work another team is doing the idea is then that you might begin conversations with that other team to discuss how best to sort these things out.
One of the easiest tools in this regard is just a “test” that blocks merging if the request is n commits behind master—just enforcing a rebase whenever you update a pull request. Combine with forbidding fast forward merges for pull requests (just let the code review tool generate a merge commit) and your `git log --graph` becomes much mor bounded in terms of how bad it can get.
Not in my experience, no.
The goal is just to keep you aware of what problems you're likely to run into if you tried to push for your change to be merged in at the present moment. If these problems are due to work another team is doing the idea is then that you might begin conversations with that other team to discuss how best to sort these things out.