I think it's a bit disrespectful to assume what others here worked on or not, to rate their answers based on the size of their projects, or based on whether others, including you, think it's a "good" practice or not. These things are always subjective from person to person, and blindly following some rules just because others do it is never healthy in the long run... especially when you already have a reasonable alternative to begin with, as emphasized above.
Having said that, I can understand the need for order and the desire to do as you want, and not as the software wants, even if it's just about something as irrelevant as a slight change of a path. On that note, have you tried using folder redirects aka shortcuts of folders to see if it's suitable in your case? I didn't test it, but if it works like that, you could have any path as the "real" or the "used" one - unless, of course, you're against even having a @Resources/Fonts folder in the first place, which would be quite... extreme, to put it lightly.
Generally, one can use a font in Windows if he installs it ("large projects" like MS Office expect the same, by the way). Rainmeter provides the possibility of not even bothering with that and just paste whatever font files one likes into a ready made @Resources/Fonts subfolder that automatically makes using them a breeze with zero extra work. Having a problem with that just because you don't like the path or want to place them into yet another sublevel (order and simplicity go hand in hand, you know) is strange, to say the least, especially when using them is not even an issue. Where would that "good folder structure" be if anyone would create his own custom font folders that anyone using the skin would have to adapt to - did you think about that?
