At best loss monitors are just relative indicators mainly due to the junk mix as you state that they run in.Logically when you are seeking efficiency using the yield monitor it is monitoring a very purified product. The loss monitor on the other hand is monitoring a very unusual combination of junk that requires a lot more luck to produce reliable information.
A friend of mine told me that he drives a pickup truck with running boards into the side of the chopper stream when he’s setting up his Class machines, and yes it’s possible to puke a lot of canola out with the straw.
If he drives beside that is multiplying collection, accuracy can only be by passing over a stopped collection area.
Except for peas I run various amount of rotor covers in all other crops balancing shoe and rotor loss with, you guessed it, the junk readings.