Technically it would still be only one quantity and not 2 different. Since the minicart.php does not affect the func.cart.php it does not matter what one likes to display there, important is only that func.cart.php remains unchanged and everything will be fine.
The cart and it's contents are not affected in any way, only the minicart would show something different.
At least that's what i've found out about the minicart.php
Anyone please correct me if i'm wrong