Can you use Inbetween to check what is the commands that the emulator sends to the rom and the rom sends back to the emulator, and then program an adapter that translates those commands back and forth to the UCI protocol?

Such an adapter would work with all ROMs that use those commands.

I did a similar job on my old 6502 chess program Usurpator II. I could obtain the source code of a 6502 emulator on the web, and fused it to a driver for WB protocol from one of my other engines. Then I loaded the emulator with the binary code of Usurpator II, scanned from a book with OCR.

Usually it is simpler to do this with WB protocol thanw ith UCI, because the way these old programs work is much closer to how WB protocol works. (They usually expect you to enter a single move, to play it and set them thinking again, rather than setting up the position from scratch every time, as UCI does.) So any adapter would just have to translate the WB "new" command to whatever command is needed to start a new game on the emulator, pass the moves in the form the emulator needs, and prefix moves produced by the emulator with "move " to get it in WB format.

I don't know this 'mess emulation system'; to make this easy, you should have a text-based emulator that can run in a command-prompt box, and accepts and prints commands and responses in text form, so that they could be sent to another program (GUI or adapter).