Upgrade to 4.7.29 causes Internal Server Error with cron
So I resolved the issue. Here's what I found. It looks like the permissions for bin have changed from 755 to 775 at some point (I looked at one of our backups and it used to be 755, but in 4.7.29 it was set to 775.)

I used this question and response:
URL for cron Jobs gives me a 404 error (not the same error, but I was desperately searching!)

Made the same changes (updated bin permissions to 755) and it all worked. So that's good (for now) but with every upgrade will we have to remember to update permissions?