Your second point is exactly why I like the bridge to have a separate tone pot to position 2 as I'm likely to roll some tone off the bridge but not as likely to roll any off position 2.
I suppose when I think about your question of what I want to accomplish, it's just to have the setup that suits me best and the fact that many people have the JV/EJ wiring (and praise it) makes me wonder if there's any advantages I'm overlooking (and could possibly benefit from) as to me it seems the other wiring I suggested would give all the advantages of the JV/EJ but with improvements.