First off, if the AI or another player has gotten that deep into your territory, then your toast anyway. So what difference at that point does it make anyway?
Not necessarily - a consolidated research station may well be treated by an enemy in the same way a superweapon is. In the most common online games, which are cramped single-system 5v5s, it would probably be very easy for a player to mass LRF or Disciples and then raid their enemy's HW and wipe out their research station and then win by attrition + ship research advantage.
Having such a high-priority single target would make players very vulnerable in the beginning, which would only increase as the game progresses and fleets get larger. A TEC player with Timed Explosives could send just 5 scouts to your HW and completely wipe out all of your research progress.
Also, I’m not saying that you can’t build more than one of these stations. Build two or three. All I’m saying is it would be nice to consolidate them.
While it would be nice for that player, I kind of like the idea of forcing players to expand and build multiple logistics research structures to get new technology.
Again, if they are that deep into your systems and destroy your research station. Then the game is over at that point.
Certainly not. A good opponent would form up a raiding party and send a bunch of ships on a suicide mission to that planet. This would be pathetically easy if the the opponent was TEC, since scouts are nearly uncatchable and can be upgraded to be immune to PJIs.