FB65,
+1 on what Bartl & PetesPonies stated. After 50 years, who knows what happened.
As for you situation, if you are dead set to have the correct rear end axle housing installed in your car, yea.....pull what you got and install the replacement correct style rear end.
If it were my Mustang, and the Mustang is not going to be used as a concours MCA (Mustang Club of America) show car where everything has to be correct, down to date codes on piece parts, paint stamps or paint marker markings.......if everything is working fine (set up, wheel well issues, cracking of the sheet metal where the top of the shocks mount to the car, u joints not wearing out pre maturely, leaf spring mount welds are holding up, no cracking for deformity with the lower shock mounts, no ride height issues, the 5 bolt pattern is the same on the front and it is on the back), shake and bake, go with what you got! You can pretty much enter almost any car show with that you have now and be ok.
I do have to say though, if it just bugs ya that the correct style housing is not in the Mustang, it would bug me also.
As for the affect of having a 67 style rear end housing in a 65 and the value of your Mustang as a whole, again......unless you confirm that your carburetor, alternator, fuel pump, radiator, engine, transmission, etc. etc. etc are all concours correct with date codes (most likely not) and or that you have a rare "K code" (271 HP) Mustang Fastback, is minimal (if it is even noticed by the next owner). But if you sell it in the future as being 65 correct but non concours/non numbers matching, yea....you have an issue there.