How to figure out what is causing the ownership of /usr/local to change from my-username to root
I had this exact same issue, and it turns out Sophos auto-update was to blame. I figured this out by running: sudo fs_usage | grep "usr/local"

It took a while, but eventually I saw Sophos's helpfully named "Installation" daemon messing with /usr/local's permissions.

I'm still trying to figure out an appropriate work around for this behavior.

EDIT: I believe Sophos has fixed this issue, see the link in the comments of this answer. It seems to be fixed for me at least!