Here's the worst story of clubhouse location that I know of.
Settindown Creek, which is the "out of town" course for Ansley GC, is a VERY good Bob Cupp design that straddles the Fulton Co/Cherokee Co. line. The course is good enough to have hosted the Nike Tour Championship, the USGA Women's Am, the GA State Open and GA State Match Play, and numerous state and national qualifiers.
When the course opened, it had a trailer that served as temporary clubhous, and the course began and ended with great par 4's. However, the proposed clubhouse site was in Cherokee Co., which did NOT have liquor licenses at that time. Fulton Co. did have liquor licenses, so after much dispute, the clubhouse was built in Fulton Co. The entrance then had to be routed through a subdivision that has no connection to the course, instead of directly off of the main road.
In order for the course to begin and end at the clubhouse, the hole numbers were completely changed, with the course beginning on a rather difficult par 5, and ending on a short, downhill par 4; neither hole is especially well-suited for where it falls in the current order. It's still a great golf course, and if you hadn't played the original sequence that Cupp laid out, it's fine. But if you did, it's hard not to feel like the course is a bit diminished by the need to locate the clubhouse near #1 and #18.
This was all years ago, and of course now, Cherokee Co DOES issue liquor licenses. Too bad for Settindown that it came too late.