It isn't really a matter of 'correct' or 'incorrect'. Either way will work. The reason for planting them deeper when you transplant is that tomatoes have the ability to grow new roots from the stem and this anchors them firmly. This does not apply to most other vegetables, although you can do it with Brassicas ie cabbage family veggies. It is especially useful for Brassicas which are going to overwinter outside as it helps them stand up to winter winds.

As Flora says, tomatoes readily root all along the stem. So, when moving my small seedlings from a flat to individual cups, I plant them as deeply as the cup allows. When setting seedlings out in the garden, I bury a good length of stem, leaving only a few sets of leaves above ground, depending on how tall the plants are. If they are really tall, I may place the lower portion of the plant horizontally in a trench. I think this allows the plants to produce a lot of roots.

Jim