When building bases you sometimes need to clear trees or bushes to be able to place base elements or tents. On next server restart the tree/bush is back again and of course clipping with the walls/tents.

Visually trees/bushes clipping with the base doesn't really matter much, but I strongly suspect collision/clipping with foliage contributes to walls not keeping AI out of bases. AI seem to mostly enter my base via the sections where there is a tree branch or something clipping through the wall.

Would it be possible to make the server check for collisions on restart and, if there is a base element or other object within 2m of its location or so, simply spawn the trees/bushes as felled or (preferably) not at all?

This is how you would construct a base irl after all, by clearing the ground to be able to build.