I know I’ve said it before, but I’ll say it again: Tomatoes love to be buried deep. If you want strong healthy tomato plants, plant them as deep as you can and transplant them more than once before they go into the garden.
I start my tomato seeds in March and by mid-April they are ready to “prick out“. I transfer my strongest seedlings, making sure they have at least one set of true leaves, to their first individual pot.
The roots are transplanted right to the bottom of the pot. Ideally I want just the leaves to appear above the soil level. If their cotyledon leaves will be buried, I snip them off beforehand.
Doing this assures the best chance for strong root formation and avoids the development of those long lanky plants with a weak stem. In a few weeks I’ll transplant them again into a deeper pot, repeating the process.