It's easy to see from the readout that the "After" runs have the engine running much leaner, which explains the lower HC and CO readings and the much higher O2 readings.
I'm not sure how a muffler would cause an engine to run leaner unless it drastically changed the O2 sensor readings... but yes, those numbers would indicate that NOx levels will be correspondingly higher. I'd like to see EGTs for that.
This is the first time I've heard of a hotter exhaust causing lean running instead of the other way around...
EDIT: Mazda uses exhaust pulse tuning to enable their SkyActiv engines to do ultra-lean burn... and I've seen really good flowing headers cause lean-running, but this is different, obviously, from a down-stream muffler that looks more restrictive than a straight through... I'd like to see if and how this creates pulses that enable better scavenging for myself before passing judgment.