The project files for IDEA have some errors and missing dependencies, as is. I'm creating a pull request for changes that I made on my forked clone to get IDEA to build cleanly (using the built-in ant plugin, not its default Make tool) and run/debug a simple jython -c "print 'Hello, world!'" all from within IDEA.
I didn't realize that guide also existed. I'll be fine doing it either way, as long as it's obvious.
The reason I did it this way was because I noticed, after cloning a clean copy, the IDEA files being there already. So I opened the project directly and noticed all the broken dependencies.
In that guide, there are even steps that first need to be done to remove the currently existing IDEA project files:
rm -rf .idea/
So if we want to go with the import-eclipse method, we might as well remove all traces of current IDEA project files from the repository.
edit: Following the guide you linked, it does indeed feel more straightforward and more maintainable in the long run. I'll open a new pull request for removing the existing IDEA artifacts from the repository.