@fgrieu although the space for FLASH is smaller than a resister, the read-out circuitry is much, much larger. It only works well because it can be shared by banks. 128-bits of FLASH is about the size of 512-bits of register (14nm SOI). That overhead is only required once though. BTW, it's probably better in older processes. 14nm SOI is weird with density as it uses DRAM for SRAM.
@bdegnan Yes. My reasoning applies if there is dense memory (for other reasons on the IC). BTW, is low-density memory (e.g. 1-bit "fuse") still a thing in modern processes? And can the state of such thing be read easily by optical means ?
@fgrieu The "e-fuse" is alive and well. You use these for IC serial numbers, and things were you wouldn't want it erased. You can optically see when a fuse is blown. Intel went away from them, but the chinese were decapping, and then using UV to erase. You generally remove the erasing circuits so they are "write once". Anyway, they quickly went back to e-fuses.
The nice thing about floating gates is that you cannot "see" the state optically, and if you put a probe to them, you lose the charge. You have to check the currents created by the floating-charge through the device.