Thanks for bringing that up. The plugin uses Room Keys to mark a logical room as already used during the current dungeon run. For example, if Map 1 has the Room Key Map 1 and gets generated, that key is saved as used. Any other entry using that same Room Key can no longer be selected until Reset Dungeon is called.
For testing, I actually copied and pasted my maps so each version had a different Map ID. I tested the system using a 3x3 dungeon layout, with a mixture of fixed and random rooms. For example, I had different copies of Map 1 for the Lower Left and Lower Right positions, and did the same for the middle and upper sections. Some rooms were fixed, including the starting area and boss area.
So as far as your question about what happens if the exact same Map ID gets generated more than once, I'm honestly not sure because I didn't test it that way. I didn't really expect developers to want the exact same map repeating throughout a dungeon. Once I get some free time, though, I'll run some tests specifically around repeated Map IDs and chests and see how it behaves