I found the solution! The operational dataset was fine, but I made a mistake with the chip-tool. When using the dataset as one of the parameters, it must be prefixed with "hex:". I was missing that. I was successfully able to add my ESP32-H2 into the Home Pod Thread network.

I've looked into this a little more and I've noticed that window, door and floor identifiers seem to stay the same across the structure builder, so it might be possible to identify a room using a floor identifier? I need to explore this more.

Did you find a work around for this? I have noticed that when converting the room's to JSON, the room identifier is omitted in most cases, which doesn't help!! I tried using a UUID in the name of the various JSON files, but once the array goes into the StructureBuilder, like you said, the room's no longer match. It's very frustrating!