Has someone done a write up on how all of the coordinate spaces and transformation matrixes work in metashape?

There is a specific problem below, but I really want the general answer so that I can solve these problems myself as I keep running into these.

I have a model of a room, it came out about ~45 degrees off level. I clearly have no way to get world coordinates mapped onto it, but on the assumption that the floor is level I rotated the bounding box so that the red side is down. I then output an orthomosaic, on "top XY", the orthomosiac was still off level by 45 degrees. Logic told me that as the red face of the bounding box is used for the bottom of a height field, it has to define the "bottom" for other things.

Next I attempted to fix this by adding some fake GCPs. I added 3 points on the floor, measured the distances between them, did a little trig in excel to produce plausible set of local meter coordinates for 3 points at Z height zero for the 3 points, entered the numbers then clicked the "update" button in reference, nothing improved.

Please advise.