Yes, that's correct. So if your Mewtwo lvX is on the verge of a KO, just super scoop up him away. You would have to wait another turn to level him up again, however.
And it obviously doesn't have to be a basic and its LV. X. You could return a Basic, Stage 1, Stage 2 and its LV. X. SSU still returns the Pokemon, LV. X or not.
If you are referring to the Base Set Scoop Up, the Lv. X is considered attached, so it would get discarded. If you mean Super Scoop Up, then it would go to your hand along with the basic.
