tl;dr: I you scp -r to your homedir, expect scp to copy not just files and directories but their permissions as well (which I think isn't all that surprising).

It's not supposed to do that unless it's newly creating the destination, or you supplied the -p flag to preserve permissions... that's what the entire issue is about; it's a bug that was fixed in 10.3.

I wouldn't even expect it on newly created stuff without the -p flag. Normal cp doesn't do it.