Because the 32X was designed to fit onto a Mega Drive, and because the shapes of the Retrode's and Mega Drive's cases are different, plugging the 32X into the Retrode (with case) might fail. For example, if the 32X extends too far back, it will collide with the Retrode's lid. Or the Retrode's case might be too high for the 32X to reach the slot contacts.
So you might be forced to take the Retrode's PCB out of its case in order to be able and plug the 32X in. I guess that's what Aleron Ives was trying to tell you.
There are screws on the bottom of the Retrode that allow you to open the case without harm. I suggest that you handle the bare PCB carefully (avoid touching contacts/solder points with your fingers). Maybe you can leave the PCB in the bottom half of the case, only removing the top and lid. Of course, unplugging the 32X may not work without touching the PCB directly.
If the problem is only the lid, you can close the case again after removing the lid.
Another advice: Connect the 32X and cartridge to the Retrode before
connecting the Retrode to the computer. Disconnect the Retrode from the computer before disconnecting the 32X or cartridge.
When you're done dumping the 32X games, you can put all the Retrode's parts back together and it should be as great-working as before.