First, let's start with the things that are good:
I like the overall design and concept of the case. It has some neat extra functions like the additional USB ports and the IR receiver. Also, the illuminated power button (two colors!) was a great surprise, as it wasn't visible on the render images on your website. I also like the interior design, how everything comes together in the small case.
But there are some serious problems with the case, as well:
Obviously, USB booting is bugged, and you will probably need a new controller. Jeff Geerling has tested a lot of controllers and USB storage solutions in his blog, so maybe you can use his knowledge to your advantage when selecting the next controller IC.
When googling for a solution for the problem, I also found that sometimes the Raspberry Pi won't boot from USB when there is a powered USB hub connected to it, as cheap USB hubs will feed back 5V to the USB output of the Raspberry Pi, and this stops the Raspi from booting. Maybe the problem with the USB boot is actually related to the USB hub IC you are using, and not to the USB-to-SATA bridge. If this is the case, you could maybe find a solution with the parts you already have in stock, by adding a single MOSFET and a resistor to keep the hub from backfeeding.
If you could post the schematics for the Deskpi Pro on Github, it would be far easier for people to find bugs like these, and to find solutions.
Furthermore, the HDMI output is problematic, sometimes I do not get any video output at all, and when I have video and lift the case, the video disappears.
Also, 4K video shows a faulty image. Both problems could also be caused by the HDMI cable that was delivered with the Deskpi Pro, as I did not test any other cable, but I assume it is more of a problem of the board routing or the microHDMI connectors.
I could not test the IR receiver, yet, but it is pretty far in the back of the case, so I assume reception will not be that good. Maybe you can also find a different position for this part when you redesign the PCBs.
There are also some mechanical problems I'd like to address:
The GPIO board that gives external access to the pins has a slight bend that will probably not affect the function of the case, but is still looking not that good.
Placing the mounting holes just a tiny bit closer to each other will probably remove that bend. Also, it seems like the 5V on the pins is only supplied by the thin FFC cable, which might cause problems with devices that draw (or deliver, like an UPS) a lot more power. Maybe the power pins of the GPIO board could also be powered from the main power source, and you can select with two jumpers where the 5V and 3V3 for the GPIO pins are coming from.
Also, the cutouts in the front and back panel are very tight. Adding 0,25mm on each side would still look good, but it would make assembly a bit easier.
Finally, the fan that was delivered with the cooler is crap. Below 100% it makes some high pitched scratching noise. I already tried to mount the fan with only one bracket in the hopes that it would stop scratching then, but even when the fan and the cooler have very little contact, the noise remains. I will replace the fan with one from Noctua.
Some people call for support for NVMe for the next board version, but I think this is counterproductive, as it would mean to drop support for SATA and 2.5 inch drives. So please stick to SATA, as this is the special thing about your case.