Thanks to everyone for their constructive (or otherwise) comments.
For us this new arrangement works for the moment at least so we are going to stick with it and make sure we can get access into the roof space in case we get any problems.
What is interesting is there seems to be no standard way to do this (look at all the different options offered in this thread) so whether you get a decent job or not depends entirely on the professionalism and integrity of the individual plumber. I'm sure loads of plumbers are absolute diamonds but ours seems like a bit of a lemon to us (soil pipe, buggered up the pressure on a new boiler, cant seem to fit a shower properly) so he wont be getting our next job.
Thanks once again, didn't think these forums worked but helped us a lot
Cheers