Hey Skeolan, thanks for the question.
The intent was to create some tactical choices and limits for the players to decide what they wanted to focus their project on.
As ever, my motto is 'your game, your rules' so feel free to tweak this as suits your game.
However, in terms of a 'ruling' rather than 'rules' approach I would suggest as long as there is some cost/consequence or risk (i.e. time and unable to go out on missions as they are focussed on a project for example) then why not? The only concern here is the 'mission' aspect is the main part of the game with the 'outpost' phase a supporting phase.
Hope that helps.