You are correct in saying that you can over compress a gasket with too high of a fastener preload. This is not desirable or required and is to be avoided by adjusting the fastener torque within it's effective range. A given fastener preload stress needs to be adjusted for this, say for a rubber, sheet teflon gasket material, or a lower strength fastener. The caveat of this is don't use a very high strength fastener for the lower preloads.
This is why a bolted flange connection needs to designed or verified by a person well versed in the art of fasteners, flanges, and gasket materials and not afraid to ask if questions arise.
The design of a bolted connection is an ongoing learning process and can be very simple and quite complex.
What you are saying was at onetime was covered by tables form the flange and an gasket manufacturers. They will still give guidelines and the proper design input parameters for a specific gasket material for you to design a bolted flange, but will shay away from actual design unless formally contracted.
Again, I'll state is all you have to do is preload the fastener to the point where you can assure that given the parameters of gasket manufacturer, code requirements including any additional operational considerations, and what the fastener material is capable of within the boundries of the it’s allowables and the gasket will be seated properly for the service conditions it will see.
This means that you, as the EOR, can set the torque value for a fastener anywhere from what is actually required by design and what is the maximum allowable stress allowed by joursdictional authority that is governing your design.
I want to emphasize that if possible you should make an effort minimize the fasteners, gasket materials and flanges if possible in order to curtail the type situation that you are now in.
Anecdotal:
The problem you are concerned with happened to us with the introduction of sheet teflon and again with the sheet graphite materials. We went from asbestos to teflon and some of the original gasket seating parameters/values for the graphite sheet were too high. We had to scream loud and long to get them corrected to match what we were seeing in the field.
There is some good information on the following website.
There are also a lot good books/publications covering bolted joints just post the fact if you desire to get more information on them.