There is no mention of head-to-head in any tie-breakers on the TSSAA website. I'm presuming that Ensworth's win over MUS in August is being ignored for II-AA M/E seeding purposes, similar to Cal/Colorado in NCAA football playing this year in a non-conference game despite both now being in the Pac-12.
According to this .pdf file, the tie-breaker is determined in this order:
1. The team with the greatest number of victories.
Ensworth and Baylor would be 9-1 and Brentwood Academy would be 8-2. BA would be punished for its loss to a very tough Trinity team out of Louisville and be the first eliminated.
The process would begin again, and Ensworth and Baylor at 9-1 would push. Baylor having beaten Ensworth 42-14 would not come into play, unless I'm wrong about head-to-head not being taken into consideration.
2. The team who plays the greatest number of team who win 50 percent or more of their games.
The TSSAA has turned the word "team" into a plural noun. Division play offsets. They played three non II-AA M/E games each:
Ensworth: MUS (6-3), Knox Webb (7-2), and Raleigh Egypt (1-8)
Baylor: Soddy-Daisy (3-6), Bradley Central (7-2), and Columbia Central (8-1)
Both would have 2-of-3 non II-AA M/E opponents with records of 50%+, so they would push.
3. The team who has the greatest number of victories over teams winning 50 percent or more of their games.
Ensworth and Baylor will have the same number, since there is no way Raleigh Egypt or Soddy-Daisy can possibly finish with a .500 or better record and their II-AA M/E opponents offset.
4. The team whose opponents have earned the most victories.
II-AA M/E play offsets.
Ensworth: 6+7+1 = 14
Baylor: 3+7+8 = 18
Even if MUS, Knox Webb, and Raleigh Egypt all win on 10/28 and Soddy-Daisy, Bradley Central, and Columbia Central all lose, it would still be Baylor with more opponent victories at 18-17. So, on the fourth tie-breaker, Baylor would get the #1 M/E seed.
It does seem unbalanced in that respect, though it would also seem unfair if the Middle/East got three byes and the West only got one, particularly if the West had two very strong teams in a given year.
The II-AA playoff format is non-traditional, to be sure, and is more akin to a college basketball conference post-season tournament than a typical high school football playoff system.