The interactive rebase command was originally designed to handle individual patch series. As such, it makes sense to exclude merge commits from the todo list, as the developer may have merged the then-current master while working on the branch, only to rebase all the commits onto master eventually (skipping the merge commits).
CONFLICT (rename/rename): Rename "will-be-renamed.txt"->"new-name-1.txt" in branch "HEAD" rename "will-be-renamed.txt"->"new-name-2.txt" in "branch2"
Automatic merge failed; fix conflicts and then commit the result.
If you want to keep one file, say new-name-2.txt:
git add new-name-2.txt
git rm new-name-1.txt will-be-renamed.txt
git commit