Persona resonance could be explained as the dichotomy between users who have obtained their Persona through the Persona game and those who have obtained them through other means (Persona 3 and 4). Plus, Rise, Mitsuru, Fuuka and Teddie can sense others who have Personas, to a limited degree.
Same for the second point: practically everyone in P1 and P2 who had a Persona played the Persona game at some point in their lives. It's a thematic difference, but not a contradictory one that those in P3 and P4 got them without playing the game.
The Strega drugs don't have much to do with that since those were used because they had their Persona forcibly awakened. The Tatsuya Scenario in Persona 2 also explores the fact that messed up stuff happens when one gets their Persona forcibly awakened.
That's really the only thing that I can see as something that doesn't make sense in P3 and P4, but the nature of what the Velvet Room is pretty much changed starting from P3.