How is that not a special base? It's only one that actually matters
I never liked, nor ever will like that "all eggs into one basket" concept. It makes no sense and there's no real risk involved.
Research should be globalized (all science labs can work on the same project, regardless of which base they are in. The magic of internet and data sharing.)
Production should be localized, so you would have production bases, with a practical limit as to how many people can work on something (simply throwing more people on something only works up to a point, especially when working on smaller things, like a rifle)
Resources should be shared between bases with the logistics abstracted. Could be as simple as a connection/line between bases that simulates supply lines. Aliens could attack those lines damaging your supply lines, which would impart temporary maluses to the base (increased production time, staff morale penalty). Would make SAM sites more valuable and give your interceptors more to do - like chasing off enemy craft. Could even generate convoy defense missions.