He seems to be discouraging signing every commit's individual data but encouraging signing the actual commit ID (SHA1) which should be perfectly feasible for something like homebrew.
You're still getting a signature directly from the developer's machine, not from the repository server and as such you're still vastly shrinking the attack surface.
You have no idea how creative people get when faced with minor nuisances. I've seen devs/admins go to great lengths to avoid doing more than one 2FA per day.