I conquered another colony with 995M population. According to your settings.txt this should have given 20 militia. But there were only 3 as it is defined in the standard settings.txt.
For a reason completely mysterious to me the game seems not to use your settings definitions.
Yes I am sure to play your mod
and the components and all other things are working as expected.
PS: I checked the population cargo space is indeed 40kT/M as you expected from your modified settings.txt file. Therefore it is only a problem with the militia not the entire settings file.