Investigate removing the ports from the case and replacing them with the ones you want. I don't know that they're the same size, but it might work. I also don't know if they're removable from a particular case.
USB3 variants have different internal connectors. 3.0 may just be faster type A, not C. Whatever way you go, make sure that what's on your mobo matches what you add, or keep using the PCIe solution. I'm guessing it needs PCIe x4, so you're using a PCIe x16 for it, with all the PCIe x1 slots sitting there just taking up space. You don't want multiple modern graphics cards anyway, unless you're doing something particularly exotic.
Cases with a lot of external-facing drive bays are available, though rare (I found 1 with 6 5.25" bays on Newegg), and they'll almost certainly not have USB-C on them. New cases are made with the intention of having multiple fans or an AIO liquid cooler on the front, so they largely give up that space. Really wide cases?
OK, I've been at this long enough that I've forgotten what it says. Enough.
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