Sure you can. I can imagine that desoldering headers with that many pins may be difficult. So if it’s too hard, send an email to [email protected] and we can sell you a board without the hearder.
If there are GPIO conflicts, you are right that you can cut the PCB trace, reconnect it to the new pin, and edit the gpio_pins.py.
Just out of curiosity, what capes are you planning to use?