All datasheets are confusing in one way or the other. The goal is to not complain (because there won't be a fix), but to train yourself to read and extract the necessary information from what you have. In many cases you need to recognize and mentally skip BS. I personally did not even know that it mention EEPROM that much until this thread forced me to read the datasheet closely. I know that no modern MCU has EEPROM and no modern MCU will ever have true EEPROM, as it is fundamentally incompatible with manufacturing processes. So, anything "EEPROM" would be emulation to a certain extent, so your goal is to figure out to what extent. And it does not take a lot of time to recognize that in case of this device it is almost none, so you can just assume you are working with the flash.
And this is the best case scenario. SAM D51 has more of a hardware-driven EEPROM emulation, and it is a total mess. Thankfully you can bypass and not use it.
As far as how address is specified - different flash controllers have different APIs, and from a lot of experience, this one is one of the better ones.
RWEE section is not present on all devices, it was added later as a way to avoid blocking while flash is written. It probably adds to confusion, but again, it is not that uncommon to have strange flash partitioning. There are some really confusing and complicated schemes out there. And there are good reasons why things are done this way, and you have to figure out a way to live with them.