Hi 2:34am. Remiss of me - I should have posted here that the KVR Waldorf forum, which includes some of the Largo 64-bit beta testers, seems to have agreed that the aftertouch issue is a bug in the VST3 64-bit version (although not in the VST2). As we are at Release Candidate 2, I'm hopeful that Waldorf will fix this before the final production release.
I was never in any doubt that Sonar was receiving Channel Pressure, as the top segment of the MIDI track meter flickers to confirm it when I press down on the keys, as you say.
To your questions, Channel Pressure can be regarded as just like any MIDI Continuous Controller - the effect it has depends entirely on how the plug-in in question is designed and how the given patch is set-up. In Largo, Channel Pressure is available in the modulation Matrix as a modulation source, so you can use it pretty much to modulate anything - pitch; filter cutoff; volume, etc. Largo also provides a special source, being LFO x Channel Pressure, which typically can be used as an alternative to using the mod wheel to create vibrato.
Poly Pressure is slightly different in that the control is particular to the key (note) that is generating it - in other words, every key that is in a Note On state is generating its own controller. As you can imagine, this places even more of a requirement for the plug-in to do something useful with the control signal. It also would imply that the player needs more digital dexterity to get the desired result. In practice, it is rarer than Channel Pressure (and none of my keyboards generates it) but IIRC Largo can use it as a mod source.
I haven't noticed any bad behaviour in patch loading, but if you say more about it, I'll take a closer look.