So I will agree that, generally speaking, some kind of real-time implementation is going to be ultimately more flexible, but it wasn't really until the Playstation that said implementations were truly trouble-free.
I basically have no disagreement there.
As a big Saturn fan, I've spent a lot of time looking into what the problem was with the system not being able to do transparencies sometimes. Basically, it comes down to the fact that true/real-time transparency effects involve two graphics having their color values averaged, and if the two graphics involved are being drawn by the Saturn's two different GPUs (or VDPs, as they're known), it's inefficient for them to communicate the necessary information.
If all you want is the Saturn's VDP2 to draw a transparent background layer of clouds over another background layer of mountains, then that's no problem at all. NiGHTS shows an interesting case of sprites being transparent over other sprites and polygons, but not backgrounds, because VDP1 was only doing the effect with its own graphics. If you want an effect like
though, you've got to allow the system a lot more processing time to pull it off because it involves VDP1 sprites
and VDP2 backgrounds. Surprisingly, this feature is also not hard to enable, it's just hard to budget time for.
Speed is the biggest reason why so many Saturn games have fake transparencies.
The bug aspect that you may have heard about is that the Saturn does tend to glitch out when doing polygon-on-polygon transparencies. The only Saturn game to do this in a non-hack fashion is Dead or Alive, and it does it only for the explosion that happens when someone goes outside the ring. The effect is so fast that it doesn't matter if it glitches.
Finally, there are hacks and shortcuts. VDP2 can make a layer of transparency over ALL graphics on the screen very easily, which is actually a very often-used effect. Also well-known is a hack that lets you make a VDP1 sprite transparent over a VDP2 background very efficiently, but with one compromise: any sprite that gets in between those two will simply disappear. Guardian Heroes did this with one character's red cape. Eventually, this hack was even implemented into Sega's later dev kits.
There, all you ever wanted to know about Saturn transparencies.