I checked the pictures of my board, and there are 3 unpopulated headers that I can see. There's also the unpopulated BIOS chip socket, which is similarly cheap. I think I would pay the extra $3 per laptop for better repairability, which is Framework's entire sales pitch anyway.
Moving to sockets adds risk of the socket failing too. But this particular instance of not using an SOIC-8, for which test clips are readily available, seems pretty unfriendly.
I imagine there's a way to program the flash from a header or connector, or maybe it was programmed before being assembled onto the PCB.