Hey El, I'm not curtain about the newer SD hotrails but the original ones were side by side coils, the new one I bought recently is sealed in plastic case but apart from the rails being wider than on the one I replaced (which I've had forever), they still apear side by side. I've seen new SD single coil sized PU using "stacked coils", I wasn't aware they worked any better than side by side for noise/hum reduction.
The basic design of a "humbucker" is to have one coil wound the opposite direction so it's 180 deg out of phase thus cancelling the 50/60hz hum (phase cancellation works more/better at low frequencies).
Another difference is in single coil strat style PUs the pole pieces are magnets (alnico generally) where in most humbucker sized PUs (but also the SD hot rails) the magnet is along the bottom and the pole pieces are metal (Iron) which bring the magnetic field to the strings. With hot rails it's one continuous metal rail inside each coil and one magnet at/along the bottom. In some humbuckers, there's a separate magnet under each coil and some just one bigger wider magnet.
But there are lots of PU designs. And if stacking coils works better ...
The new SD silver series looks interesting where they are using silver coil wire rather than copper ($$$ though) but silver is a better conductor than copper and used quite a bit in very high end (very expensive) audio cables. I know a guy who spent $6k on 2 x RCA <> RCA short patch leads (I think for his SuperAudio player to preamp).