Believe you me - if I could afford a 6 BBL car or a HEMI bird I'd grab one in a minute but the simple fact is they demand the premium prices by the simple "supply and demand" model. Fewer were made (and fewer survive today) which makes them much more rare - and therefore more valuable to the collector than the typical 383 powered model. Each has its price point and each is rare in it's own right - it's just that some are more rare than others.
Take mine for instance. It has quite a nice option list as noted below (+ indicates equipment my car came with):
According To Galen Govier Production figures for the Roadrunner hardtop are as follows;
1969 Roadrunner hardtop shipments to USA 46,868
1969 Roadrunner hardtop shipments w/E63 (383 4-bbl 335 hp V8) 99.1% 46,446 +
1969 Roadrunner hardtop shipments w/S77 (Power Steering) 50.6% 23,715 +
1969 Roadrunner hardtop shipments w/E63 & D21
(383 4-bbl 335 hp & 4-speed) 45.5% 21,325 +
1969 Roadrunner hardtop shipments w/G33
(LH Remote Outside Mirror) 34.3% 16,076
1969 Roadrunner hardtop shipments w/C55 (Bucket Seats) 31.5% 14,763 +
1969 Roadrunner hardtop shipments w/H51 (Air Conditioning) 10.8% 5,062 +
1969 Roadrunner hardtop shipments w/A36
(Performance Axle Package) 9.8% 4,593 +
1969 Roadrunner hardtop shipments w/E63, D21 & A36
(383, 4-speed & Performance Axle Package) 6.2% 2,906 +
1969 Roadrunner hardtop shipments w/B41 & B51
(Power Disc Brakes) 5.1% 2,390 +
1969 Roadrunner hardtop shipments w/H31 (Rear Defogger) 3.3% 1,547 +
1969 Roadrunner hardtop shipments w/R21 (AM/FM Radio) 2.4% 1,125 +
Note: Roadrunners with a/c were equipped with the 330hp 383 4 bbl engine - not the 335hp engine. So my car does not technically qualify as a 335hp and 4-speed combo but few people know that.
Now, as a 383 road runner my car is very rare due to the options (the Perf. Axle Package also included 3.55 Sure Grip rear and max. cooling option used on the Hemi cars. My car was also ordered with the Hemi suspension) but it will never be worth what a 440 6BBL or Hemi car in comparable condition is worth because it is not as desireable. It's rare - but not as desireable as it's big inch brethren. Desireability is what makes certain cars more expensive than others of the same breed when there were more than just a few manufactured.
Now, would I heavily modify a real 383 road runner? Maybe, maybe not. This car of mine would make a great 6 BBL or Hemi clone (except for the a/c) since it has all the underpinnings and if I had the $$$ it would be sporting such a powerplant because it would be simple to revert back to stock. Would I cut it up and make a pro street car out of it? Not me, but I would understand if someone chose to do so with their car, especially if it was a stripper like my first one.
I guess my take is this - yes, they are all "rare" - it's just that some are more "rare" than others and therefore command a higher price if you desire one.