I've always wondered about this myself.
Most level maker software will allow you to create collision boxes. Usually those are the more expensive Oriented Bounding Boxes (OBB's) rather than Axis Aligned Bound Boxes. So, that's obviously one way to go; create a program that lets you assign them by drawing them, then store that data with your model. For assigning bounding boxes, you almost have to use OBB's since AABB's prevent you from changing the orientation of your model. You "might" get away with a 90 degree rotation if it's a cube because it would then be axis aligned again. But if it's a box instead of a cube even a strict 90 degree rotation will mess it up.
I've dreamed of using Blender for collision geometry. Under ViewPort Shading there is a bounding box option. That makes me wonder if you can set bounding boxes for objects in Blender.
But that aside, you could create another mesh as a box, give it a specific name like, "Bounding Box", and then load it into your game. The way I am currently working, I'm writing my own custom Python exporter for the model data, and so I could easily tell it to just export this in the file as bounding box data rather than as a mesh. Then I'm using my own custom model importer in C++ where I can have it read that data from the file and if I had a bounding box member in my model class, I could have it assign the correct values. But this makes a lot of assumption about you having full control over the situation. If you are working in Unity by exporting an FBX file, you may have to come up with a different plan. This is one of the advantages of writing your own because you have complete control and can add in anything you want.
If you could find the two vertices that are the furthest from one another, I think you might be able to calculate a center point for the model. Then you could calculate a bounding sphere. I would probably do that first. I think bounding sphere collision combined with OBB's might function pretty well even if you have to check a large number of collisions. The sphere check is extremely efficient, even noticeably more than AABB's. Only when two objects intersect on their spherical collision do you even need to check the OBB's. So, even though that's a fairly expensive check, you likely only have to do it in cases where there is a very high probability of collision.