It’s something of a mystery indeed but often happens as I remember back 3 or 5 years ago when the VW Touran was on the scheme and the SEL was the top of the range model but had an equal or lower AP than the 2 models that were priced lower in the retail market. Although that is a reverse of your statement as the more expensive model has the cheaper AP its still an oddity with no reasoning.
It could be a number of reasons like a new model the manufacturer wants to be seen out on the road, as a sort of advertisement or could be end of production with a new model coming out or simply Motability did a good or bad job in negotiating but this last theory is normally met, if its a good negotiating, with the manufacturer withdrawing the model from MB for a few months only to return with a greater AP later.
My current car is a VW Tiguan R-Line that had a greater AP than the Elegance and although the retail price difference is only a couple of hundred £’s the lesser Elegance was the go for model as it had thousands of £’s of extras on it over the more expensive R-Line and one of the reasons, I think, the Elegance was withdrawn for MB back then because VW knew with a new Tiguan about to be release that they could shift the old Elegance with all it’s extras easier than the nice looking but less extra’s old R-Line.
I would of loved a Tiguan PHEV (who wouldn’t want a car doing a possible 190 MPG) but alas these we’re way too expensive for us and with private Joe’s falling over themselves to get a hand on the PHEV version puts the AP 2, 3 or 4 times higher so there’s no saving over the short time we have these cars.
Just my thoughts that could be way of canter. ?