I asked Brandmeister / DMR+ a very long time ago and they both said they do not validate the Repeater ID. They both send the Repeater ID of the connected client in messages MST -> RPT. I checked the source for MMDMV / DMRGateway sometime ago and whilst it conforms to the standard when sending a frame, it's a bit more liberal when receiving them, and doesn't validate the Repeater ID.
The MMDVM protocol was only ever intended to be "single hop" so I think it's a safe assumption that the intention was for the Repeater ID to be that of the last hop.
Overwriting it will work, but I think there is some value in having the actual source repeater ID when chaining applications together, such as confbridge and the parrot. That way you can see the source of the transmission to the Parrot in its own logs rather than just the ID of the confbridge.