I can help with some of those.
1. What does section attribute "crew" do?
2. Is there any way to make DN sections individually destructible?
3. Why are stations divided into 3 sections with virtually identical stats?
4. Is there any way to rebalance farcasting (range, +- etc)
5. Is there a way to rebalance the species specific research efficiencies? (as listed on wiki: http://wiki.swordofthestars.com/sots1/Research
6. Is there any way to turn off the auto-grant of techs to Morrigi at game start? (cyber & robotics)
7. What does REBELAI_COLOR_FLASH do?
1. Affects boarding chances when boarding pods latch on. More crew = more resistance to boarding (though there are race-specific factors as well.)
2. Dunno but doubtful. The largest ships (DNs for SotS1) are only destructible as a unit in order to represent that they are innately tougher than other ships due to their size & bulk.
3. Presumably so that you can destroy a piece of the station without killing the whole station. Stations are not built with armour or the same degree of general toughness as DNs.
4. I'd look into strategyvars for this, but I don't recall seeing anything there for farcasting, so probably not? Not certain tho.
5. IIRC this is moddable in SotS2 but not in SotS1.
6. IIRC these are granted by links in the master tech list which cost 0 for Morrigi and are not available for other races; those costs can be adjusted. But Morrigi are already pretty weak economically in the early game, and their economic productivity is balanced around not being able to research Cyber Interfaces because they start with it.
7. When an AI rebellion occurs, the planets that rebelled flash, so I'd imagine this plays a role at that time.