The best thing? If you run the #16 heads with dished pistons you will have the advantage of using heads you already have. A '68 GTO with the correct heads on it is a nice thing.
However if you run flat-top pistons with 6X-4 heads you have the option of swapping to a higher compression head later if you like. The 6X heads already have hardened exhaust seats from the factory for running unleaded fuel, the #16 heads do not (but they can be installed during the rebuild). Dished pistons will not allow you to up the compression as much later to a certain extent.
Both ways will work, your choice.
Wow, just saw the pic of your '68, gonna be quite a project!
Your daughter is very lucky to have a dad that is so dedicated to doing her project car up right like that. Good luck.