I disagree. And I have also done "my military duty", as if that signified anything.
Yes, Xenonauts are a secret organization, but not so secret that there is a chance that their existence is still in question to the aliens after the first few missions. Xenonauts are also a Guerilla organization against a vastly superior enemy. Do guerillas centralize all their assets so the superior enemy can take them out in one sweep? Maybe you should use your brain (just mirroring your borderline insulting argument style here). So, for me, multiple bases in this scenario make much more sense. If you now call them "big" or "small" or whatever does not really have a meaning in my opinion.