For me, the only difference between the two is the amount of reward you get by completing them (in some games it’s less balanced, rewarding “mission success/failure” to primary and a lot less to secondary), I just simply like the idea of not having a primary, “mission-failure” objective, instead you get rewarded for whatever you did, even getting intel on a newly built Hive can be crucial, even if you couldn’t destroy it, and lots of “secondary” objectives are similar to that.
There are players who just simply don’t want to play a game where they don’t see the HP/details, see HP visibility thread, and excluding a relative big part of the TBS playerbase is not the greatest move in my opinion, even if the game less mainstream than FiraXCOMs, a really niche game will get less additional content from the devs (like underwater missions!), so I would rather have more options/some compromise instead.
Your “Phoenix Project Haven” does work, contains information, you “just” don’t know what happened to the rest (communication failed for too long), so knowing the basic shape of your surroundings sounds not that farfetched for me. Sure, you may not know how exactly the “mission site” looks like, but that’s battlescope, not geoscope. If the geoscope was procedurally generated too, I could somewhat see the benefit, but as far as I know, “only” the havens will be randomized (so you don’t know where other havens are), Earth will remain more or less Earth-like. You still get the Explore from 4X, just not the basic geography but the man-made changes.