You can make your bases totally immune to spawns and events. But it takes some work.

Not sure about flying events messing with crops... that might be something you just have to deal with.

First to prevent spawns inside you need 100% coverage of spawn preventing items like workbenches... any tiny gap will allow group spawns inside.

Next you want a wall around the outside. This is less for defense and more to block line of sight. Enemies will not attack if they don't see anything to aggro on.

An important factor here is how your base is located. You should not build a base where enemies will have the terrain advantage on you. Optimally you want your base to cover the peak of a hill.

Out from the wall you want a series of moats or drop-offs <drop off if on a hilltop> spaced apart from each other and the wall. This area should also have spawn prevention coverage but you will need to hide the benches or whatever so they don't get attacked. Bury them or enclose them in shelter so they are not seen. <or resign yourself to repair/replace regularly>

Keep everything in base covered except farm area.

Nothing can spawn inside

If an event happens they will spawn but just stand outside and do nothing. Just crouch for the closed eye icon and wait it out. Nothing should attack. If they do from hearing a noise they will often toss a couple of rocks then stop if the see/hear nothing.

After the event ends you can just clean up the remainder.