My prefence for hutch with pipe connecting to run rather than hutch with underrun is that i feel hutches with underruns are a bit unnatural. Someone a while back pointed out to me that "If a rabbit is frightened instinct tells it to get underground into a warren, whereas with a hutch over a run the most covered/sheltered/best hidy area is up a ramp. So its like the opposite of what instinct tells them to do" - i had to agree with this statement, it makes a lot of sense and certainly ties in with the behaviour i've seen from my buns - i.e. it doesnt matter what hide boxes there are in the run, if they are frightened they run to their pipe, and if they are upstairs in the hutch, unless they are already most of the way into the bedroom compartment when they get scared, they turn, run down the ramp and either into the tunnel or the dark part of the hutch downstairs.
I also feel the pipe from the hutch seems to add a lot of enrichment to their environment too (more so than just having pipes in the run). The other benefit of a seperate run attached by only a pipe, is it can be moved around the garden easily.