Basically, the difference, besides the potential quality of the LEDs, is the fact that with fixtures that use discrete RGBLED sources, they rely on distance to blend these three colors into one uniform color. Unfortunately, with so many point sources, they will never blend perfectly and there is always a chance for shadowing. Basically, if you stand in front of the beam, you may see many shadows of yourself in red, green and blue.
Theoretically, tri fixtures eliminate this problem by combining the three colors inside the LED itself and with a reflector and lens. Is it perfect? Maybe not, but it's certainly better.
Also, the Tri fixtures you are looking at are brighter and have a wider beam angle, though understandably more expensive.
As a note, both fixtures use Red, Green and Blue for additive color mixing, so your question is really more about the type of LEDs used.
I'd see if anywhere local might have them in stock that you can see them side by side. Without knowing exactly what you're doing, I can't guarantee the added price of the Tri will be worth it, though my gut tells me to stay away from the SlimPar 64s.