I only check the "respect tile resources" and leave everything else unchecked, focus on balance. I gave the sector (4 new planets) around 2k each of energy and minerals. I did check on them from time to time and build things (clear tile blockers, build pop) but I didn't notice anything at first.
But, because I'm playing a DA machine empire, I have specialized robots for each resource and I que robots for all the tiles after clearing the tile blockers according to tile resources. I only build 2 buildings before getting to 5 pops (for growth and unity). The AI usually builds some level 1 buildings until I get to 5 pop because reason.
For example on a planet I have like 5 energy tiles , 5 mineral and 5 research. Because the sector AI likes to move the pop around non stop I wait for all the robots to be build and than put them on the right tiles. But, now I have 8 mineral buildings, 5 science and 2 energy so it doesn't add up. I check every tile and there are mineral (in this example) buildings on energy tiles.
This should not happen regardless of the shortages or whatever, at least in theory. That's why that damn check is there. It used to work like that, now it doesn't, at least for me. I don't use any mods.