First, UE4 is not yet officially supported as a platform where the Editor can be run on. It says nowhere it would work fine.
It works because Epic and some good ppl in the community work on it, but its not there for general consumption yet.
Then what you experience as a bug is the same behaviour everywhere, and not a bug. Windows, Mac, Linux. You create the C++ project, the project launcher closes and the IDE starts with your project. The Editor is going to use your C++ code as libraries to present itself and your logic, that must be built first. Fully expected behaviour.
If you want it to work fine you should go try it on Windows until its ready for Linux.
When you delete the Intermediates folder you got to regenerate to project, and it will fill up again when you build the Engine. My Windows build uses around 35 GB, more if it starts collecting backups and asset caches and what not.