I also don't understand the reasoning behind not caring if 3rd party apps are not able to be skinnned.
When I use my PC I am running programs. If you leave out the apps well, your just using your PC to click around the OS and not actually doing much with it.
Since Day 1 of Windowblinds there has always been programs that did their own thing and WB wouldn't apply to them properly. Nothing there has changed, only the culprits [usually].
The OS Shell is what needs skinning, along with open windows [as much as is possible].
There is absolutely no way on earth that any one developer can possibly manage to create a program which actually can skin ALL programs' windows. It cannot be done and never will.....although it is fair to say 'most' could, once upon a time.
The current diversity in programs' "styles" is possibly our own collective fault....showing programmers that their proggies do not have to be so butt-ugly...and simply hope that the OS shell can clean it up a bit.
It wasn't even Nullsoft who originally started [much of] it all with Winamp ... it was an outsider called Fly7e. Even in that specific case it was a direct result of my meddling with 'magic pink' that Maxim came out with a proggy that would code the Winamp Transparencies for the skinner [Instead I had done it the long way which took a heck of a while to do... but it showed the way for Maxim's proggy].
Moving on several years later you had the likes of The Skins Factory doing really cool stuff with WMP .... I'm still using their Alienware 'ALX' ... [it's still fun] proving the MS default was just 'yawn'.
Early days saw a lot of people actively involved in totally alternate Shells - just about the best way to avoid most of the MS 'dross', but again MS reinventing themselves made more problems for outsiders to keep up...and interest dwindled [certainly did for me].
Lately I've been skinning FSX [another living-in-the-past proggy that can be skun [I like that word]], and avoiding tweaking the MS OS....can't even run WB with FSX loaded/running....and you need it running when drawing the graphics and re-applying.
Of course, when I did use LiteSTEP you only had the Windows in WB to apply [the Explorer shell wasn't running] so all my WB skins looked a bit crap because they were really only for the 'windows'.....[and they were crap anyway]...