Except if you have difference with the main product in the CSV, then yes, probably on import it will recalculate automatically and you get not what you want.
If you have combination’s final price in the CSV, then my suggestion above will work. Main product is not a separate product anymore. Combination is separate (physical) product. So if you set weights and prices as they are in CSV, you get what you want. Customer can’t choose product without combination, neither it is used in the lists or anywhere else, default combination is used instead.