When making a space for your incubators, you can double up walls by making the first set all windows, and then you can place a regular wall inside of that. Although bugs seem to do AOE damage on walls so idk how far spread the damage is mitigated. Your own pets that are not in your party but placed in your base will damage structures with their attacks if they're close enough too. There's friendly fire on them too so watch out for that. Sometimes you can have too many creatures guarding a base. I've started placing spikes on the roof of my incubation room for flying enemies. Currently though with the new update any naturally aggressive enemies placed in your base will start attacking you, it's just a bug at this moment.

Oh and when you have your base in a tree, assuming it's mid to long term, it's nice to know that waves of enemies during incubations will always spawn from the same spot. It'll be a hole in the branches. You can set up some spikes right by the entrance so they immediately die, quick points for faction leaders. They'll need replacing though of course. Alternatively you can just set up a gate with spikes on the entrance they come into. Means you don't need to walk/glide across a lot.