Except that it's not a must-have. Or are you saying you've never completely cleared out a POI without being on a clear quest where all the enemies are clearly marked for you? If we're talking about good and bad design, we have to separate ourselves from our own experiences and wants and look at it from a bird's eye view, and think about the most benefit for the most people. Maybe you think having clearly marked enemies is a must-have, but given you only have that during clear quests and we're not seeing a lot of complaining about that, I don't think that's a well thought-out opinion.
That said, it's still an opinion worth thinking about, which is why I addressed your concern about finding that one Zed that moves. The only ones that move are the ones you trigger yourself (or someone else with you), so the only scenario your specific frustration comes to play in is also taken care of by the same perk. It makes sense for the Perception tree, for immersion, and for a natural extension of the player's abilities. Do you have another concern? I can try and mold the concept further if need be.
It's also worth noting that the only quests that are affected by the radar in this way are Clear and Fetch/Clear quests, which represent only a fraction of quests. Even then, only rank 4 and rank 5 quests go to sufficiently large POIs to have this problem. If you're relying on quests enough for that, you'd already be specializing toward making them easier, wouldn't you? It makes sense that you'd spec some Perception, and as such, a perk that would help you sense nearby threats.