Trans Am & Malibu are rather special cases: these are so well known that the car is often known only by that name rather than the base model name.

It was not really the body of the Mach 1 that was different. One could order a fastback bodied Mustang that was not a non-Mach 1. http://bradbarnett.net/mustangs/timeline/69-70/69/

There are some on the site that have "Mach 1" as the trim level (which I think would be more appropriate), and others that have it as part of the model. As you can see there are many variations of Mustang http://en.wikipedia.org/wiki/Ford_Mustang_Variants , so how do we decide which are important enough to make part of model name? I guess when the site change is later extended to trim levels/versions this will be a moot point. When that happens, I assume that Mach 1, Trans Am, Malibu, GTI, etc. would best be located in the trim field?

Usually we put "important" trim levels in model name, like the Trans Am for the Firebird, Malibu for the Chevelle or the GTI for 80s European cars, as many people will search for these.
I do not know if Mach 1 can be considered important enough, but the car body was a little different, isn't it? So it can be justified.

It seems that most on the site have Mach 1 as part of the vehicle model, when it was really just a trim level for the Mustang and not an entirely separate model. I just wanted to check and see beforehand if there were any objections or reasons that these should not be modified so that "Ford Mustang" is the model and "Mach 1" goes in the trim level field.

As an added benefit if they were changed, then all of any given year would display together. In my opinion that would be better than how it displays now with some in order by year and then the Mach 1s at the end of the list. Those at the end could be missed by someone searching for Mustangs of a given year, unless they knew to look at the very end of the search results.