I have never used EEPROMs as a UV eraser costs just a few bucks and therefore 'normal' EPROMs are easy to re-use.
The conundrum with your incompatibility stems from the feud between Cloanto (3.X) vs. Hyperion (3.1.4, 3.2), i guess.
Maybe it is not intentional and there is just a specific ROM part missing.
