Ya, basically when you put in a Probinator, your literally replacing the chip in the ECU that controls the fuel maps and VRIS points, so it's not a trick or a bypass, your literally putting in a new chip with the new configuation, and you can put that chip into any compatible Mx-3/Mx-6/626/Probe ECU.
When you order your Probinator ECU, you tell him what your running for motor and what intake manifold and he'll program it accordingly. ZE ECU's are still up there, but have dropped a bit in value. There's currently one for sale for $90:
http://www.mx-3.com/phpBB3/viewtopic.php?f=2&t=66925" onclick="window.open(this.href);return false;
I've heard mixed opinions about the Probinator about passing emission test, but I know from my experience on my car that it ran richer, but it also feel better and has a broader powerband since the VRIS points are corrected for the curved neck IM.
Yes, you have to match the ECU and VAF. There's a few tricks like running a KL02 (KLDE) VAF on a K8 ECU and it seems to work well for what I've heard. The JE50 VAF that comes on the V6 Mx-3 is the proper (yes indeed) ECU for the KLZE ECUs.
I did my own Probinator, it's not bad, but on mine, becuase the ECUs are old, despite how well i desoldered it and several traces tore up with the chip. I wasn't too happy about that and I was easilly able to repair it, but most who aren't electronically inclined may not or may not be comfortable with that.