To support having Shifted Boss (i.e. boss in area unlocks that area), we create extra copies of each boss in each area. These are stored at the end of the room data. When Samus is in one of these rooms, the pause map shows that you are in a room which is not on the normal map. My suggestion would be that we show a room with a dot for all boss rooms.

vs showing the normal big room with another room with a dot next to it for the item

Using a single tile will allow us to easily fit the boss rooms anywhere. We will need the code to be smart enough to draw Samus in our single tile the whole time you are in the boss room and/or item room. Plus we need to consider how this impacts multitroid.
This idea seems complicated to me, but I don't have a better idea at the moment. Suggestions welcome!
NOTE: No need for a dot in Phantoon rooms because there is no item.
To support having Shifted Boss (i.e. boss in area unlocks that area), we create extra copies of each boss in each area. These are stored at the end of the room data. When Samus is in one of these rooms, the pause map shows that you are in a room which is not on the normal map. My suggestion would be that we show a room with a dot for all boss rooms.
vs showing the normal big room with another room with a dot next to it for the item
Using a single tile will allow us to easily fit the boss rooms anywhere. We will need the code to be smart enough to draw Samus in our single tile the whole time you are in the boss room and/or item room. Plus we need to consider how this impacts multitroid.
This idea seems complicated to me, but I don't have a better idea at the moment. Suggestions welcome!
NOTE: No need for a dot in Phantoon rooms because there is no item.