I was in same boat as you even though I read about XPz quite a lot before starting a playthrough. 400 hour investment sure warrants some investigation before full commitment. Still feel overwhelmed, after one month of intensive playing and just 17% research progress (max possible brainers ofc). Got an endless research list in main base to prove it. You can peak into
online BootyPedia to avoid some disappointments (like Dream Library). Best beginner help I got was from
The Newbie Guide. After about 1 in-game year you'll basically learn everything to be well on your own.
Here are the answers to your questions and some personal advice (I'm also on middle difficulty):
I shoot down 150 ships of most fractions - no base attacks. Not even a mission to seek one out. Although I read people experienced being invaded as soon as February. One full-proof tip to survive: have 20+ soldiers and as many Hammers. Yes, day-1 hammers... It is capable in killing anything, even end-game enemies, with relative ease. Maybe Dioxine just loves Thor, dunno. Alternative is to rely on proven save/load technique and use more sensibly equipped squad.
Glimpsing all ships is fine. Only Govt ships are no-no regarding shooting down. Civilian, if they incur any penalty I never noticed - only killing actual civs on the battlefield (stunning is OK tho).
I used to kill fellow mutants (and Lokknars) because they looked like the enemy, lmao. Score penalty is negligible so that at least made for a fun learning experience. RIP many Lamias, Brutes & Bugeyes. You learn these things in time. The only real show-stoppers I can see are unwinnable main base attacks, and out of radar range enemy activities (can combat with just plain research to offset negativne score those incur). For the first prepare Hammers, and just research stuff for the latter (not as serious as I was made to think frankly).
Just research, don't worry about order. Researching yields both score and money (at end of month). Personally I prioritize: radars, craft, craft weapons, soldier armor, soldier weapon. Simultaneously going for more brainer capacity facilities, Omlette du Fromage (for money), exhausting prisoner research (prison space is actually the main enemy in this game).
Pogroms I believe incur -100 penalty before Mutan Alliance, then -1000. Help Lokknars is also -100 (but do them for apples). Any mission of such penalty will have it stated when you click the pink dot I think. Also 100 penalty is nothing, 1000 is about 25% of income in early game. When you make 25k score a month even 1000 are skippable if you can't be arsed.
Don't worry about spoilage. There's so many things to discover a few spoilers won't make a dent in your experience, only prevent frustration. In fact my position is that hiding basic game mechanics behind those #research numbers is dumb and worst part of the mod (unreasonable difficulty spikes being close 2nd). Probably had to be done to water down technological advancement from prisoners though.
That's about it. The biggest challenge in your case would be understanding underlying original game engine mechanic the mod expands upon. I dove into XPz after recently playing original UFO/TFTD for about 4 months and becoming sort of an expert. Only needed a few additional questions and be on my way. So far it's my top 5 game of all time. The incredible imagination, complexity and depth far outweigh any issues that gripe me.