1. Well I never did start a military base I will have to try that now. If you use the ministers the title matters because they use that to tell them what facilities to build on that planet. Otherwise I didn't think it made a difference but maybe you found something new
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2. Counterintelligence only works if some other race is using intelligence actions against you and you use enough points to stop that action. It seems to work the whole time it is being "researched". If no other races had built intel facilities it will fail.