hi,

if I pop out the RD2 chip from the emulator itself, and replace it with an ED2 chip, will
writing to the internal eeprom (not flash) work the way it does on the ED2, even though I'm using a RD2 emulator?

if you mean migration from T89C51RD2 to AT89C51ED2 then you should read this datasheet - look at pages 3 and 4 where it shows the differences between EEPROM usage on both derivatives.
In short, software which is made for writting EEPROM of T89C51RD2 will not work on AT89C51ED2. EEPROM read access is the same for both parts.

Regards,
Oleg