Perhaps since they have multiple spi and i2c interfaces onboard you can spare one easily and you can pick the size you want, but my guess is that it is also a process thing.
They rather spent the surface to more RAM and Flash since those need to be on chip to be as fast accessible as possible while eeprom is already slow. One thing I do know, the die is the same in a subfamily if it has 64kB or 320kB RAM, same die they just OTP fuse out access to the extra RAM , ROM.