I use to spend all my time developing it, but I've had to try to get other things moving as well. I want to continue developing it, but there are various realities I'm facing that make it difficult at the current moment. I hope people can be understanding of that. This doesn't mean that I won't update it- just that it might take a while.
In crocotile3d, everything is basically a square tile (two triangles). When you export to obj, there is an option to merge the vertices. As for creating collision boxes, I'm not sure what the standard method for those are. In my own game experiments, I have created an object in the scene that I can hide/show, and place tiles in it where I want collisions, floor, etc. I then exported that object to obj, and used that to test collisions against.
That's how I would do it- split your scene up so that you have a specific object that holds a bunch of tiles that will be checked for collisions, etc.