I can't quote your post so :
on farms and population:
farms are only usefull to raise the population cap of the planet. Beware that raising population will raise insatisfaction unless you build morale improving structures or have morale resource starbases or lower your taxes.
The population determines your level of taxes as well, so it's a good thing. I think it can also impact your production (military and social), but I'm not sure
Starbases.
I think you can overlap their "bonuses zone" up to a point. There probably is a cap.
Logistics determine the number of ships you can have in a fleet and the number of starbases you can have. Your mining habilities are determined by your tech level and installed modules
Defenses
When your defense is not the one designed for a certain weapon (like gun with armor, laser and shields) then its effect is lowered. instead of a defense of 2 for armor, when attacked by a laser ship, the actual defense value will be sqrt2, so 1,14 so 1. (it is rounded down).
Resources affect the entire empire
You can create fleets by stacking ships, then selecting them and clicking on create fleet. No need to be over a starbase. And yes, fleets protecting military support starbases are very efficient.
Hope this helps