Throw in a PCIe switch or something so you can still attach a USB 3 controller and now you've doubled the price and power consumption.
SD cards are not all designed or optimized around small, random reads and writes - the typical workload of a boot drive - and latencies can be staggering. Similar for USB sticks. On the other hand, these days the overwhelming majority of M.2 SSDs are at least somewhat optimized for 4K IOPS. The latest Sabrent Rocket M2 SSDs get some 650,000 4K IOPS vs eMMC at ~13000 (the Rocket is 50X faster) an SD card around ~2000 (the Rocket is 325X faster).
Frankly if you stuck a Sabrent Rocket on a PCIe 1.0 x1 connector the performance would absolute savage an SD or eMMC solution on this workload. Even if they somehow also had identical sequential I/O specs.
And hopefully that would ensure the new form factor to be somewhat stable for a while after that.
you have to keep in mind the original goal of the raspberry pi project.
if you want nice performance and low power consumption, you're better off considering a cheap intel nuc.
SD card: $15.20 for 128GB on Amazon
The price difference is minimal.
But the SSD is much much faster in that price range.
But they walk a fine balance with PCB space, backward compatibility, performance, cost and user-friendliness.