Actually, there is no EEPROM in the SoC. The ROM firmware is, well, a true mask ROM (the first stage), and the rest is loaded from external NAND flash. It's actually impractical to put EEPROM onto the same chip as a modern high-end SoC: it would be too cost-prohibitive or take too long to develop, because EEPROM needs special processing steps that regular CMOS chips don't. You'll never find EEPROM/Flash on a leading edge, high-end process, it's always older stuff. This is why eFuses and other OTP technologies are used, because some of them can be done without any special processing steps. And why just about any decently powerful device always has a little 8-pin flash chip to hold the firmware next to the main SoC. You only get embedded flash with low-end microcontrollers.
Some (particularly older) OTP chips are just EPROM (one "E") - the kind you erase with UV light - without the UV window. EEPROM is actually UV-erasable too, and one of the things often done to reset security "fuses" in EEPROM-based microcontrollers is to apply UV light in the right spot. Chip designers end up using shield metal above the bits, sometimes not very successfully (I recall one such chip was hacked by putting the light at an angle to get in under the upper metal shield). But this is the realm of lower-end microcontrollers with embedded EEPROM/Flash.