Yes, of course. you are right. If we don't have conflicts because of the content (either because contents are equal or conflict-free mergeable) then we should avoid reporting a conflict for mode changes happening on one side only.
And additionally: If we create new content through a content merge then we have to decide on a filemode for that new file revision. Also here we should do a better solution then just picking the first filemode we find as I do now in getFileMode():
I'll propose a fix for that