My guess is that it's a genetic dud, with how the lower stem is swelling significantly in the center and there is no proper growth tip forming. There is energy going up but it can't extend. I see stuff like this occasionally too, its usually pretty random. Some times two starter leaves grow and nothing forms between them, I see it in beans as well as toms. I would tend to think the seedling is perishing because its simply unable to grow with those genetics.
This question opens the door to an existential side of tomato growing.My husband grew this from a package of tomato seeds, is confused by it looking like Frankenstein's monster, and wants to know if it is even a tomato and why it looks like this.