http://www.latibulum.com/pvk/proportions/
There's no way to get rid of the system-wide warnings without removing them. They represent the benefits of having vestiges of an actual civilization in a system. A system without anything but military and industrial facilities is going to have certain disadvantages, represented by missing out on bonuses to happiness, research, etc.
I will probably be adding some more intermediate steps to the urban facilities, and might end up re-naming some of them, and making a couple of tweaks, but basically the idea is to make it take a lot of time, effort, and expense to develop a major colony. Considering cities (representing more than just "a town") can be established in a couple of years with enough work, it seems more or less what I was shooting for.
Although, another thing it helps to realize is that much of my reduction to the Ratings of facilities is an attempt to reject the simple additive logic of SE4. Adding a lab on a remote planet isn't going to really directly add to the research speed of the whole empire directly, the way the game logic works. Similarly, adding a mine in a distant colony is not going to magically provide those resources to an empire - there is a lot of redundancy and expense before the empire will see any net gain, realistically, and practically in this mod.
PvK