Early EEPROM could only be wiped entirely (but as this was done electrically, it was still an improvement over UV-erased EPROM), while EEPROM at the time of Flash's creation could often be byte-erased (as is the case now).
Nowadays "EEPROM" mostly refers to small, slow, rarely written config storage for microcontrollers. As thus, they are also usually accompanied by low write/erase endurance despite their byte-erase granularity.
Flash was meant as a higher capacity/performance version indeed sporting full block erasure as a downside, but nowadays it has supplanted EEPROM in all categories but small micro-controller usages. Plus, as capacity is now cheap, high write loads can easily be supported with write levelling (that is, writing to new locations instead of erasing/writing the same block over an over.)
So every time you write to three same byte you're writing the same cell. 100.000 cycles is actually much more than current flash generations.