Yes, I tried growing onions in shallow stuff and I know what you mean. Taller would be probably better, but as you can see tomatoes can tolerate mushiness quite well (unlike onions).
I thought the classic EB mix was one where you add about 1/3 or more bark fines. So promix + 1/3 bark fines, maybe even more perlite (it will help for sure but you need to get to a % where it actually matters).
I grow in mostly peat but it's top watered (manually) so a different story, it gets to partly dry between waterings.
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