Is it possible to leave the choice up to us by making it a configuration option? I realize it's more cost effective to go with a single solution. However, for the people that have a board with the new USB header, they'd probably be willing to spend extra to take advantage of the extra speed/power it brings. Utilizing the new header is more expensive than just using the old one, so those who need/want it should bear the extra costs. Additionally, by making it modular, if and when we upgrade to a board that has the new header, we can simply order the other IO module from you and swap it out.
Regardless of which option you decide to go with, I still think keeping a single USB Type-A and Type-C port is the best solution for the foreseeable future. I definitely want to keep the 3.5mm audio jacks. They're such a convenience, why does everyone always want to do away with them!? A lot of motherboards include op-amps that improve front/rear audio or both. I'd hate to lose access to such a feature.