No, because you are still balancing them. The charger dictates the end voltage, not the way the pack is constructed. Assuming the balance lead is wired correctly and the charger is able to charge each cell independently, then the main contributor to how your packs balance is the charger. This is of course assuming the pack itself is healthy.

That's the whole point of balance-charging. If it didn't work that way, then why would we pay extra money for a charger that can also balance? Back in the day when LiPo tech was new to the RC world, you would have a separate device to balance the packs. Charging LiPo batteries was a lot more of a pain in the ass back then.