I don't think it's a case of beating a dead horse. However, upon further reflection, I have to tend to agree with the current way of listing them. Take a look at the Central Planning District system, which is an EDACS network encompassing Lynchburg, Amherst County, and Bedford County. This is a five site system, and all talk groups are listed on the page for each of the member sub-systems. It does seem to be logical to list them this way, since they are inter-related. One merely has to place the sites in different banks (or groups if you have a 396), just as you have done. That way you can listen to whichever ones you desire and/or can pick up.
I think the Central Planning District is a better comparison than is Fredericksburg and Spotsylvania, which share little in common as far as their respective systems, other than some mutual aid capabilities. However, they do provide backup for one another should there be a catastrophic failure, just as Fauquier and Culpeper would do.