I see what you mean, I agree. I wouldn't worry about the conservation of mass as this is covered with the lore but even if it wouldn't, I think that the fun should come first.
Right now you can clear the area although it's not just about checking all the places to shoot everything but more like killing a specific number of enemies that can come to you anyways. I will most likely keep it this way. I haven't yet decided if I want to have spawning pools per zone or share them between a few.
What I do strongly agree is that such a system might be frustrating and seem to be unfair. Making it that the robots are not spawned in the places you already explored is not an issue as well. As the system already knows what did you see.
But then, I think that it might be easier to make the game feel more fair to the player with a dynamic spawning system. Imagine you're low on health/ammo and you have to cover a specific distance to get to the healing/ammo station. In many games you're just knee deep in... trouble. Doom solved that by allowing to refill ammo with a chainsaw and health through glory kills or if low on health. This really works but only if you can move quickly and find the right target. Also because of that, Doom uses dynamic spawning to provide a low tier enemies to fill up your ammo/health. Arena shooters work with that quite well. Enemies don't have to spawn out of thin air, they can crawl through holes, jump over walls, fall through the windows etc. I worked on Gears of War: Judgment and we had a dynamic spawn system too with places marked specifically to spawn with an animation. For other spawns we used small e-holes, so the enemies could crawl out of the ground.
Back to the example - so imagine you're low on stuff. With dynamic spawning you may have a system that sees that and allows you to get to a safe place by spawning less enemies or not spawning them at all. This as a story, would work much better in your head if you didn't know it was scripted, so it's better to not make it happen all the time. But when you have a way to control if such things happen, you might be better than with traditional spawning.
It might be also easier to mix the enemies, so in the areas that allow this for happen you may have ranged enemies then melee, then back to range, then a different kind of ranged. Especially if you have an open-world.
What annoys me with some linear shooters is that you end up with an obstacle, for example an arena. And you have to deal with it. You can't get smarter, go around it. Every single encounter has to be finished. Ideally this should work as "you had a hard encounter, you had problems with it, you got better, you did it, you felt relief". In real world it leads to rage quits. While I do really really enjoy already mentioned Doom (both 2016 and Eternal), I had a moments in which I just thought "I can't have this anymore". I closed the game and got back to it after a while. Just because anything else felt not as good as Doom's core gameplay. I have to admit that some arenas that were a problem turned into a logic puzzle in which I was optimising the encounters. But I do prefer doing that during a normal course of play than being forced to only to progress.
One of the core aspects of TFG is adjusting to the play area. This requires procedural generation. This brings us to "it's hard to script encounters with such confined spaces". What works in Doom might be much much harder to do here. With a dynamic spawning system at least I may try to spawn enemies in order, so the difficulty increases, instead of being a game of hide and seek where you try to find hidden enemies to fight them.
It's actually to try things out, the previous spawning system is still there and it's easy to replace one with another.
The better system will be kept in the game.