Yes, BUT, wouldn't a collector want a car that was one of only 300 made, unlike the GT500? They made less 2000 Cobra R's than they did 2009 GT500KR's
Don't confuse rarity with value. Just because a vehicle is "rare" doesn't exactly mean that it's "valuable".
You must also consider brand dillution. Like Miatas, there are dozens of super duper special edition special mach anniversary whatever edition mustangs. A quick search online shows the T-5, High Country Special, Ski Country Special, Challenger, Cobra II, SVO, SSP, Bullitt, Warriors in Pink, Anniversary edition, etc.
10 years after release, how many of these "special" revs command a significant premium over their slightly less rare counterpart? IMO, the big money maker for these special editions is a) the mfg b/c of a higher invoice price and b) the dealer because of the markup they can sucker out of the first buyer.
How many of these special editions achieve the collectability of say a GT350-H? A: not many.
At the end of the day, it's still a Mustang and for every "rare" factory model, there are dozens if not hundreds of slightly differentiated cars. Like it or not, that WILL impact collectable/resale value.
IIRC, they made fewer late 90s early 2000's Z3 Coupes than they did M coupes (the car than looks like a civic hatchback snuck up and mated with a Z3 convertible). Did that increase the resale value of the lower performance Z3? Nope.