You know things happen, and sometimes one thing leads to another. A bad "new battery" can be a reality. Also did they test your alternator? Boiling a battery generally indicated a messed up alternator, or a bad "new" battery but I'd have a electrical vehicle shop do a real load test.
Why did they only replace one battery? It almost sounds like they never tested the 2nd battery which would be a huge mistake.
Do you think the battery positions were swapped when they reinstalled them?
The reason I asked if Ford did it is because how difficult it is to pull both batteries and test each
on its own. Rarely do they do this and instead just hook up a tester to the system where the good battery masks the problem. Been there and done that
A boiling battery is the key phrase.
Good luck.