I think CSG is overly complex and heavy for this type of thing. If you’re interested in writing you’re own converter I’d look into writing your own slicing logic or something out there that’s more light weight. Clipping geometry with a plane or box isn’t as complex as it seems. You really just need a function to slice a triangle into it’s component parts, convert the quad component to two triangles, and determine which side of the plane the triangles you want to keep are on. Creating decimated or lower level of detail tiles is the more complicated piece, though, but there should be libraries for that, too.
It looks like there are existing open source tools on Github for converting to 3d tiles, though, if you look through the 3d-tiles and 3dtiles tags. Keep in mind I haven’t used any of these and can’t vouch for any of them but it looks like there are command line tools to convert OBJ or GLTF to a hierarchical 3d tiles format. Perhaps you can use or build upon these?