The reference point could be any point, but the purpose is for example if you copy a drawing of a wheel it makes sense to choose the hub/axis as reference point, so when you reinsert it you can place it properly.
The other query: I can not confirm/reproduce this behaviour. Maybe the layer of not copied entities is locked?
In my exercise I draw three different bodies. circle/triangle/square side by side
Each one with a different color(layer). I then select them all go to copy/move.
When they do…. all three appear in the color of the layer that is shown as being active ??!!
Since you cannot duplicate this scenario I wonder if anything in my options/settings is out of whack ?!
I wonder if anyone else encountered this same problem ??
I fooled around a bit more trying to solve my problem and here is what I found…!
I found that by using the Move / Copy (two trees) symbol on the toolbar the result is the loss of layer transfer as described before (only the active layer/color is transferred). When using the copy and paste (two gravestones in the menu bar..?!) the different layers are transferred intact. EXAMPLE: 3 different bodies in 3 different layers (colors) – no Snaps applied / select all 3 – left-click on COPY then left-click on PASTE and only then decide on the desired SNAP. Move the 3 bodies into position. Click ESCAPE to maintain the original (COPY) or DELETE to MOVE
I don’t know if that makes sense, but I works for me !