I keep all my raw files in git-annex. I wouldn't say that it is effortless, you need to have a good understand of git, but if you do, it works really well and is extremely flexible. Raw files go in git annex and sidecar files (XMP, PP3) go into git itself.
I thought that article was quite lazy. It was a long winded way of saying "I opened some photos in each application and compared the out-of-the-box rendering to LightRoom, but made no further effort to try and see what might make these applications worthwhile."
Impulse noise reduction in RawTherapee is pretty good.
For darktable, there was some changes to noise reduction a few releases ago, and its now recommended to use two instances of the profiled denoise module, on that targets luma noise and one that targets chroma noise. It also works pretty well.
Neither work as well as the DxO prime, which is the best noise reduction I've ever seen.