So, as far as I know the storyling of Generation zero goes like this:
Main Game > Alpine Unrest > FNIX Rising > Resistance Update
I think progressing throught the game would feel much more natural, immersive and new player friendly if missions would actually unlock in the canon order.
So once you complete “Behind the Curtain” you unlock “Not alone”, once you complete “The Resistance” you unlock “Where the Sun sets”, and once you complete “Wages of Fear” you unlock “Good News”.
Of course, if you don’t have one or both DLCs, you shouldn’t be required to buy them both to access FNIX Rising or the Resistance Update, so in that case I think it would be best if those chapters are skipped, so for example if you only have FNIX Rising you would go straight from main game to second DLC.
Of course, one downside would be that this would gate base building behinds hours of gameplay, which might be undesirable.