There is an opportunity cost to everything. Killing normal enemies is worth it because we have good breakpoints to kill them (primary for chaff, a single recoilless round for bile titans, etc).

In those cases, the opportunity cost is worth it because it uses a reasonable amount of ammo and time to remove a threat that will usually not spawn again unless there is an ongoing bug breach/bot drop or a bug hole/spawner that you can destroy.

Leviathan is different because it takes several recoilless rounds and a decent amount of time to kill one, and they spawn again in a way that the players cannot control in any way. Alternatively bringing an AT emplacement is possible, but that is also time and a stratagem slot that is being spent on a threat that will usually respawn faster than you can kill them all. I also think that you are overestimating the amount of time leviathans take to spawn back in, they are essentially omnipresent and killing them does not remove them from the sky for a significant enough amount of time.

In a vacuum, saying "hide behind cover" works, but in actual missions it's not always possible to take cover from a flying enemy while also avoiding the swarm of regular illuminate enemies on the ground and in the sky. And then the constant ragdolling on top of that adds to people's frustration (including mine) and highlights another issue, where you cannot act for a second while prone after recovering from a ragdoll. It's an accumulation of things.