Air Carrier pilot voiced concern regarding ATC routing assignments with regard to direct airport vs. VOR; when identifications are the same.

Narrative

I have a safety concern to which I have been unable to find an acceptable resolution. It concerns clearances that we are given on flights to airports with off-airport VOR's by the same name as the destination airport. The best example is departing MSP and given a clearance to 'Rochester' by ZZZ center. This clearance is ambiguous; it is not clear whether we are cleared to the VOR or the airport. I have spoken to several instructor pilots and many Captains. The opinions vary. Some say the VOR; others the airport; and others say it depends upon the weather at the destination airport; VFR vs. IFR. Others say it depends upon how we are filed and whether or not the FMS is operational. Most feel quite strongly about their opinion. I have twice spoken with MSP ARTCC on the telephone and inquired as to what they mean by this type of clearance. The answers I got were different both times. My personal opinion is consistent with what the first center controller told me; 'It always means the VOR.' He further explained that when our airspace system was designed we only had the capability to navigate to a VOR and therefore could not navigate direct to an airport. I personally like this definition because if the weather is worse than expected at the destination; the VOR is typically an IAF for an approach. After my initial telephone conversation with the center controller I felt confident that it always meant the VOR unless specified otherwise. I got so much resistance from many captains that I felt compelled to call ARTCC a second time. During the second phone call I was told it means the airport unless the VOR is specifically stated. Wanting an accurate confirmation I called the technical support line and asked if they could tell me where this clearance is defined in writing e.g.; FAR's; AIM; Air Traffic Controller's Handbook; etc. After several discussions and e-mails the consensus from them is that this type of clearance is not defined and if any question exists I should query the controller. Asking the controller for confirmation is always a good idea but not always practical or even possible. For example; departing ZZZ for RST during a big push when everyone is deviating due to bad weather the frequency is almost too busy to make normal transmissions let alone request confirmations. I feel an unnecessary and unacceptable level of risk exists by introducing the possibility of an aircraft going to someplace the controller does not expect. Several months ago I was enroute to RST from ZZZ as the pilot not flying. We had been given a long series of vectors and then clearance to 'Rochester' I asked the Captain to confirm my selection of the VOR in the FMS; and he disagreed. He selected the airport. We were getting close to RST and the frequency was busy. Eventually I managed a confirmation and the controller responded with irritation; 'the VOR.' I would like to help address this safety concern but I'm not sure of where to best begin. This ambiguity is unnecessary; unsafe and very easy to solve. We simply need a definition of what this clearance means; or in the absence of this we simply need the controllers to state in the initial clearance VOR or Airport.