Thought i'd post an update in case anyone reads this thread in the future. I had another play with the rear tub today. It seems that I had been hasty before - the top of the Equinox panel fits nicely, it's the bottom that was wider. After a bit of a prod I've come to the opinion that this is because there is no structural rigidity in the panel - so it flexes - I am guessing that as the sides flare outward at the bottom the back of the panel bows in a little...
I think once I trim it all to fit (I am doing the rear roll bar stays to Book spec - so can't actually get the panel on without cutting chunks out of it) and actually clamp it in place the sides will fit nicely - and squarely.
So I don't need to worry about spacing out my side panels either. Hurrah!