Hi Simon,
1: EEPROM data set size and partiton codes
The Valid EEPROM Data Set Size Codes and Valid FlexNVM Partition Codes in the document K20P144M120SF3RM, Rev. 3 is not correct. Our document team already found this problem and will update it.
Please refer to the older document about this part, just link this:

The PE configuration is correct:the partition code is 0x07 and the data set size value is 0x30.
I also attach the older reference manual for your reference.
2. Question about 'This read-only bitfield is reserved and each bit will always be read as one'.
The bit is read-only, so even you write it, it can't be change, and always be read as one, it is just for bit6, bit7, but EESPLIT and EEESIZE should be write, then the EEPROM data set size is 0X30, EESPLIT(bit4, and bit5) is 0b11, EEESIZE(bit0 to 3) is 0b0000.