Questions

[Suicide Junkie]

In cargo is the same as deployed to the planet.
As long as you're not trying to store them in orbital bases, they will work just fine.

Base maintenance is in the settings.txt
If you want full control, you could set the base maintenance to zero, and then add a negative resource generation ability (use the one that is independent of planet value!) to the facilities. Set the description to mention maintenance costs, and you're golden.
This has the additional benefit of making the construction and maintenance costs independent. For example, you could have a power plant that costs metal to build, but uses up 500 organics and generates 1500 rads each turn.

Start with Kwok's Balance Mod AI scripts. And don't play finite resources against AIs. It won't work well unless you're willing to put in a lot of work to make them act completely different.
You'll want to play against humans in order to make a finite resource game practical.

Settings.txt again. The minimum/maximum resources for various start options are listed in there.