I think a lot of it comes down to money. For Fox to budget and green light $150m on 2 movies might be expecting a bit much.
This way, if 'ALIEN: Covenant' bombs - or breaks even - they're not risking a further $150m on another movie that not only MUST be successful but make up the differences, shortfalls and losses of the first one. It's just too much to ask. If 'A:C' is successful, we'll see a sequel to 'Covenant' - not Blomkamp's Quarter of a Century old overdue sequel.
People are divided over Blomkamp's proposal as it is. Some want it. Some don't. That's no guarantee for success.
Would've been Great...