For surface scan missions:
What would be, if they would work right? For each mission a separate landing point and separate progress of the mission? Not "scan one to complete 20" but "scan 20 points at 20 planets to complete 20 missions"
This would solve the problem without nerf in any direction
Nailed it. Having all missions (with different destinations) complete from one location is just another one of those bugs that frustratingly doesn't get fixed for ages, and players get used to it being part of the game.
Just fix the (major) bugs first, then see if the mechanism actually needs to be drastically changed. What the OP describes is probably how it's supposed to work for all we know.