Some of your points seem valid, some I've covered and some are batshit crazy. Just kidding, I can understand your concerns but I disagree with your opinion on some of your points.
I am guessing that you're concerned that "Collectable Contacts" means that there are fewer players visible to the rest of us in the game. I agree, that's not good news. We want the world to seem active and we're starting from a low enough bar as it is. That said, a lot of people already spend all their time in their base.
1. Agree. 2. Agree. 3. Agree 4. Disagree - why not use phasing?
One issue that hasn't been covered (except perhaps Rudra's issue #2 above) is that of Supergroups. I feel like the system would work fine if the base were only there for one person, but what about guests? What about other Supergroup members? What if one person has unlocked a dood for the base but another hasn't met them yet? What if they've met them but only done half their arc, etc. Obviously, these aren't questions I can answer here, I'm just pitching an idea and I haven't thought of every possibility.
What if players find one of their contacts visiting their friend's Supergroup base? Would that be cool? I think so...
I think this system has a lot of scope for giving players a reason to do missions from obscure contacts, or to explore more, looking for weirdos and oddballs hiding in the corners, the ones you don't usually visit. I imagine someone asking, "where did you get that person from? They look cool, I want them for my base, too".