"It seems you can't trust the manufacturers to be faithful to the prototype?"
As a former employee of Bowser Manufacturing, I must respectfully disagree with this statement. The outright lack of understanding reflected in some of these comments is huge.
You need to understand there were literally thousands of F units built; they were one of the diesels that vanquished steam, and of those thousands of F units, Santa Fe had the largest fleet. Books have been written that focus heavily on modeling just the Santa Fe F units. Like many railroads, the Santa Fe units had countless variations and upgrades over their lifetime as money-earning machines. As others have stated above, you have to look at a specific unit in a specific year or few years to get any of the Santa Fe F Unit models "correct". Especially on Santa Fe, F-3's were upgraded so that externally they look like F-7's, and roof fans of various sizes could appear on any Santa Fe F unit. There's so much more to modeling Santa Fe F units than just the single vs. double headlight issue.
If a manufacturer is going to sell an F unit--ANY F unit--at a reasonable price point that most folks could afford, just which ONE particular version should they do? Tooling costs money--why should Athearn do separate low priced models in Santa Fe--I bet fans of every other railroad might want their road's F unit instead of a Santa Fe version. Research time and tooling costs money--money that isn't there for low priced models. When they already own paid for tooling that brings in profit, why should they upgrade it?--instead Athearn chose to offer, for those who demanded it, an entirely separate line of locomotives that is largely correct for each railroad offered.
Athearn is being incredibly accurate with their Genesis F unit models--they didn't model just the rare early 1970's Santa Fe yellowbonnet version, but instead modeled at least 3 different variations of the paint scheme on A units, all of which are photodocumented as being exactly correct--with the correct horns, lights, nose rings, and other details uniquely correct for each individual unit. Now sometimes Athearn's assembly fit and finish may not be quite up to par on an individual unit you find in a store--but then the Proto 2000 F units are exceptional in that department--however, they do not generally offer all the road specific details of the Athearn Genesis units. Instead they usually focus on as-delivered or (in the case of Santa Fe, 1950's era) versions with less modifications, but that is changing.
Finally the various manufacturers have done a tremendous job of modeling the F units in disgusting detail. If you search long enough on Ebay, you can find really nice models of F units in most of the prototype paint schemes, as they have been produced in HO, or are coming out soon.
I use Athearn Genesis, Intermountain, and Proto 2000 F Units on my layout, depending on the paint scheme my son "has to have".
Perhaps Athearn might one day upgrade the basic F-7 tooling--but others (like Walthers Proto 1000 line) already have done so. It probably makes more economic sense for them to do completely different models that the other guys don't already have.