Flash/EEPROM endurance
It's the same basic principle.  These type of insulated gate stored charge memory cells can be made with various tradeoffs.  Generally those called EEPROM are optimized for more write cycles and individual access, while "flash" is optimized for high density and therefore lower cost.  Compare the ratio of the number of "EEPROM" bits versus "flash" bits on the same chip.  It would be too expensive to implement the large main processor memory with the same devices as what they call EEPROM.  Also compare the write and erase block sizes to see another difference.

Actually flash is just a type of EEPROM, since EEPROM stands for Electrically Erasable Programmable Read Only Memory.  Flash is largely a marketing term for a insulated gate stored charge non-volatile EEPROM optimized for a certain set of characteristics.