This is getting confusing with all these "Ryan..." replies, given the presence of two of us
Sure, ideally these three items would come in a distant second to building the best possible course - I wonder if there are places where the 1st and 18th greens are nowhere near the clubhouse, and the Nines don't return.
Stone Eagle comes immediately to mind, but the bar area serves as stand-in clubhouse here.
Taking it one step further, what if the best routing dictates that the 18th hole leaves you somewhere other than where you started your round. Any good examples?
Industry Hills Zaharias is the closest thing I can think of...though the lateral distance between 18 green and the clubhouse is not far, the climb of several hundred feet places the 18th green probably a half mile from the clubhouse once you're done walking it (since the Funicular has been DOA for years)
Re: the 3 or 6 hole loop...It's kind of an odd idea...even if it happens incidentally, it still throws me for a loop, no pun intended. I just played Fazio's Primm Valley this weekend, a 36 hole facility on the CA/NV border en route to Vegas from LA, and the Lakes course returns to the clubhouse at 9 and then at 15, taking you on a 4-3-4 triangle loop for the closing stretch. Interestingly, while this was a bit odd for my tastes, I felt those three holes were three of the best on the course and were I a member with 30 minutes to kill, I'd gladly jump onto the 16th tee and play three quick ones.