These include semgrep, ast-grep, LLMs, and one-off scripts. After running these tools on a large code-base, you usually end up with lots of additional unintended changes. These range from formatting/whitespace to unrequested modifications by LLMs.

Maybe LLMs do, but why would semgrep or your one-off script be making unrelated changes? This is like using sed to replace something and using grep to filter out the very things you just specifically modified. It should be unnecessary if you commit frequently enough and don’t do 10 different refactorings before starting to commit each one.