I think you bit off a bit more than you can chew this time.
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No really, it all sounds and looks good but that's a massive outline. Some of the stuff is about stuff not directly related (containment/attack options) and some of it is dependant on people going along with other parts in the form you propose.
The reduction formulas are unnecessary. 60 people seems to be a pretty full base (though with labs and workshops going in increments of 10, how did you get 12 and 24? I've never had more than 4 pilots at a base either.) but they don't all have to be there. There's more than 8 or 10 people in most cities, most of them just cleared away from the aliens already. Likewise some of your personnel are going to be off base on their day off, doing off-site work, or safely whisked away to safer shelters as the UFO approaches. Simply add the spawn points to the lab, etc. and let the map generator add workers/scientists semi-randomly like it does civilians. It'll be capped at the number of spawns or your total workers.
Now I don't actually think you need any bonuses for those workers. An base attack is not really something to be concerned about right now. It's almost like them giving you a UFO. No risk to civilians and not much chance they'll weaken your base if you complete the mission. Also right now there's no preassure on your supply of workers and scientists. Just let them be killable. The point of base defense should be trying to keep them alive. The reactor and containment stuff will be good but I think just making the workers and scientists "base civilians" would go a long way.
If they are too have skills and benefits let them occur during non-combat.
The extra soldiers, the armoury, maybe. A bit much but I could see it. The armory would be waiting on the dropship inventory system to be implemented first I'd think.