1) I can confirm that 3 layer mapping is supported. All mapping is basically done through the RPGMaker XP interface and then there's some script that debugs them so the transitions are seamless. All events are also done through the event editor, which brings me to your next question
2) Poccil's I'm pretty sure has a script to make healing happen in Pokemon Centers and through your Mom. You'd just reuse that script on a different NPC/switch to make it happen. Scripting your own character effect events probably doesn't work like you think, because Poccil's doesn't use RPG Maker's "Actors" interface, so I don't think there really are characters to have effects on. But most conceivable things should be possible and present in the scripts available.