You raise some good points.
XP1LM is just GTR10R, isn't it? So, no point counting it twice...even though it is at McLaren HQ, I believe it would be sold if someone offered the right sum. So, I think it should be put into the GTRs as one of the "active" ones.
I think the Le Mans winning car is the only one that Ron Denis would never part with.
As for frequency of use, it doesn't matter. As long as they are not rotting away in a garage or museum, you can consider them "in use" even if it's stretching the term in some cases.