Optical audio is somewhat an abandoned standard. The copper port is as good. And professionals use external devices connected to USB and synced in their digital audio workstation software now.
USB-C gets somewhat more frequent now. But USB-A is the mechanically superior standard for sort-of fixed installation (like on the back of a PC). And if you have a USB-C device, chances are, you also have an adapter already.
Thunderbolt is pretty niche. It's more a mac thing. It's nice to have - but 99.9% of the users don't have any matching devices and routing those PCIe lanes to a PCIe slot is better.
It is somewhat a hot take - I know. But if you really use the 2.5 G Ethernet, you probably want 10 G anyway. So just go for a board with that or add it via PCIe card.