I'll try to explain, however I'm no guitar maker or acoustic engineer so it might be quite technically inaccurate... Let's begin:
As you can see, there are 3 single-coil pickups on a Stratocaster. In this case, each pickup possesses 6 permanent magnetic pole-pieces that are located under each strings.
diagram of a single-coil pickup
When a string is vibrating, it creates variations of the magnetic field maintained between the coil and the string thus creating an electric signal sent via the guitar's jack (output).
Now, since every string has a different diameter, each permanent magnetic pole-piece is designed and ajusted (in height for example) specifically for each string.
Yet, Hendrix was playing with a right-handed Strat and mounting his string in reverse order so he could play it left-hand. Consequently, each strings on Jimi's guitar were over the wrong permanent magnetic pole-piece, resulting in a slightly modified sound.
I think this is (one of) the reason(s) he kept playing on a reversed right-handed Stratocaster. However, there might be some other personnal reasons he had and that I'm unaware of.