So there really is a progrom penalty? Is it -400 without the research and -1000 with it?
I ignored a progrom and still got a positive month. There were hardly any events but I was raiding a lot of landed/splashed UFOs so it seems that the "don't raid civilians" rule really is wrong and doesn't lead to point loss. I've got 3 more bases coming up which will have a sharkbike 50mm cannon in each one. I'll also build a workshop and living quarters in one of them so it can manufacture the ammunition, and my main base can eventually convert into an alcohol production base (though I'll continue to use it as my main base as it has the laboratory and that's something I can never replace, it'll be game over if I lose it
The advice was very specific: do not research Mutant Alliance until you have global reach. Meaning, until you have a craft that can reach every point on the globe. Case in point: in my early months, I had a few missions, including a pogrom, that my Airbus simply could not get to. The advice was quite solid. Once you research MA, you gotta at the very least fly to each pogrom and start the mission. Pre-MA, not getting to a pogrom carries 0 penalty. Post MA, you get a flat -1000. If you do touch down and start the mission, you get the regular mission score. In case of a pogrom, immediately retreating you get negatives for civilians killed by aliens, and that's it - which is always less than 1000.
Far as civilian traffic goes, it is a matter of preference, but after nabbing a couple freighters with no kills, and getting -100-something for each, and not that much of a haul, I figured it better to leave them be. There seems to be no shortage of other traffic.