You don't really need to separate them until your final transplant, but it's probably better to do it beforehand, if you have the time and resources.
The seedlings will be fine in the same container, but they'll use up the nutrients faster, and they won't grow as large. When you separate them, they should get a growth spurt soon afterward to get to the size they would have been had they been separated earlier (that's my experience).
Don't keep them together after the final transplant, however. That can often cause production to go down significantly (but the plants should be fine foliage-wise).
However, as alphazero inferred, you might have more success if you just cut off the extras per container, and let one grow with undisturbed roots. However, you can still grow tomatoes fine if the roots have been disturbed at some point (they do heal), but plants with less disturbance might do better. I've done both and have had success with both (and I'm not sure, but it seems like the undisturbed ones were earlier and grew faster). If they're determinate, I'd probably recommend avoiding disturbing the roots.