Hi niko, yes extrude along path curve will work with auto booleans, all methods of extrudes including extrude by path, extrude tapered, and extrude to point will auto boolean when it's a face selected as the object to be extruded.

I've attached an example file - in the example file select the circular face, then run Extrude, pick the "Set path" button, and then pick the path curve. You should see that will generate an extrusion that's been automatically boolean unioned onto the base object. Same thing if you use the "Tapered" or "To point" options as well.

If you're having problems with it not working with a particular file can you please post the file or e-mail it to me at moi@moi3d.com so I can take a look?

- Michael