I just LOVE garden experiments, LOL!
I have to agree with Joannabanana. The extra depth you created in batch "A" is allowing more roots to grow along those stems. You're gonna get stronger plants from that batch.
When you are ready to harden them off before transplanting, here's a neat trick. Lay the cans/cups on their sides, and leave them there. The plants will naturally turn themselves upward toward the sun, and make an "L" shape. Dig a deep trench for transplanting, and set your "L"-shaped stems down with just the tips of the tomatoes above the surface. Your plants will form roots all along every part of the stem that's buried underground, for a nice, strong root system.
You shouldn't have a lot of transplant shock, and they'll take off rather quickly.
Hugs!
