I'll take a look if there is increase in penalties on larger number of cities. In my first game I had 16 before the end, but didn't check specifically if penalty was 32% or larger. Doubt it, but you never know.
I don't see what would removing fortress bonuses accomplish other then force EVERYONE to have few cities at most or have their production completely halted. From what I saw, the whole mechanic is geared toward slowing down expansion and penalizing pioneer spam at the start of the game. Also, there is population cost for pioneers so it limits the spam even further.
I don't really think that example of 20 cities really works that way in game. If you start with -15% unrest penalty then everyone else, that means that you have -15% on growth, production and research from the very start of the game and that snowballs into other empires producing, researching and growing faster then you. They are far more likely to get to said 20 cities with LOWER unrest then you with no outside influence. Also, you rarely have opportunity from monsters and other factions to grow a lot cities at the start which means you have to make do with starting cities who produce 15% less then everyone else.
I really don't see how mechanics that force you to build balanced city be POINTLESS. I mean, the whole point of the system is that you need all the elements in it. This is actually great system, the only thing needed is that AI needs to adopt to it.