Roughly 78,000 packages already comply with the
pds/skeletonstandard, although they may not know it. To formally show that your package has adopted the standard, “require-dev” it via Composer, or display a badge on your README.
WordPress kind of assumes that the whole project is public, so you don’t really get public/ folder. It also organizes the code into wp-includes/, wp-admin/ and wp-content/ folders, instead of the src/ suggested by PDS. And, in terms of configuration, everything goes into wp-config.php file instead of something in the config/ folder.
CakePHP is much closer to PDS in terms of organization of files. The only difference that I can spot is the use of webroot/ folder instead of the suggested public/.
I’d really love to see larger libraries and frameworks adhere to the PDS, but until that happens, I’ll keep an eye on things.
P.S.: The standards comic strip is of course from xkcd.