As yet, Ras, it's got no further than what you see in the photo, a mockup, but the point you make is a good one. Cutting the "hooks" the end board of the truck slides into would set the crane a few mm further back, and this would improve clearance. If not, it would have to be the last wagon on the train, as you suggest.
EDIT: In fact, I only tried this out after seeing the other version using the big yellow crane because I'd got the vehicle in pieces to wash after buying it. It's in excellent condition, so if I was to make the custom, I'd try and find one in poorer condition or even just someone selling the rear section and the crane parts.