You seem to be under the impression that there are two Micro USB ports on the Pyra and replacing one of them with a USB C would be easily done.
There is a full function microUSB 3.0 OTG port AND a microUSB charging only port.
The MicroUSB 3.0 OTG port is the wider one. This one has a ton of tricks up it's sleeves. It can be either a host to other devices OR can be set to make the Pyra a device for another computer. It can run at the maximum speeds that the Pyra's SoC is capable of communicating at allowing for hubs, gigabit ethernet adapters and more - but you will likely need to purchase a microUSB OTG adapter - they're readily available online.
The 'other' microUSB port is a charging and debug port. It is not capable of 'normal' USB operations. It exists so that the Pyra can be charged via commonly available microUSB cables while other stuff is connected to the microUSB 3.0 OTG port. There are some hidden data capabilities in this one, but they are not USB spec - more like a set of debug pins.
There are two more USB type A ports.
One is a USB 2.0 port with USB 2.0 functionality.
The other is a USB 3.0 port with USB 2.0 functionality and the other 4 pins used for eSATA.
However, replacing any of those with a USB C port would result in absolutely no gain in function or capability. Without a major redesign of the main board (especially charging circuits) AND a new SoC board, it would be an aesthetic USB C port only. It would have none of the capabilities that yield benefits from USB C (fast charging, alternate modes (display port & HDMI), faster data).
You seem to have obsessed over ED mentioning it as a possible consideration when prompted by a userland question. I think it is great that he considers these things. He also said that he would like to replace the entire back of the Pyra with a metal plate similar to ATX computer motherboard fitments so that changes in port configuration would be easier. He also mentioned that he would like to make the device 2-3 mm thinner and have a more custom-sized heat sink. Lots of ideas. Ideas are good to consider.
By the time the mainboard, SoC board and case are redesigned and properly re-worked to incorporate a USB C port and it's related expected functionality, it would probably be better to simply start over from the ground up (or nearly so) on the next version of the device. I expect that to be 2-3+ years away if ever. For that to even be a consideration, this device, the Pyra, will need to sell in self-justifying and sequel-justifying quantities. Sitting on the sidelines waiting for a USB C version of the Pyra is likely a very long wait for a bus that never runs.