Seems to me among other things, having made a semi-cursory read of the article, that much of the incompatibility/interoperability of similar tools made by different developers is easily circumvented by simply choosing a current, stable, established distro. This in itself is the solution to having all your tools working the way you want, and a tool for every job.
Personally, after having spent a number of years watching 'wizards' and 'configuration tools' borking my system and 'fixing' things such they are subsequently inoperable and unfixable without repeated variations of the input into said 'wizards', I strongly prefer the manual method of configuring things. I love it!
The article, while well written, is as the author stated, somewhat incomplete. It doesn't really consider that there are hundreds (likely) of WIDELY varying distros of Linux, compared with very few versions of the competition, each of which is 90% the same as the last release.
Linux to me emitomizes variety, personal preference, configurability, customizability (??) and functionality. And there's a distro which affords pretty much any combination of these qualitites in varying degrees, from ragged-edge to perfect.
I also don't think it's fair to compare the file organization/location of Windows vs. Linux. Sure, Windows puts more stuff in one/a few similar places across its versions, but it doesn't help the system *work* any better! It merely allows for a small problem at one moment to mutate into a huge problem.
A few extra minutes spent locating config files for something, after one is familiar with ones preferred distro, is to me preferable over being at the mercy of hidden/cryptic/delicate registries and such, requiring unsupported tools, wizards, and "DO NOT EDIT" message boxes.