Most modern software uses .config, and I suspect the holdouts are due to cross-platform support issues. Windows may have it's own equivalents, but they are radically different from Unix. Developers may not want to deal with those differences, or don't want to deal with the support issues related to those differences.

The remaining holdouts tend to be very old applications. (The XDG standards are less than 25 years old, then you have to give time for them to be adopted.) For some of those applications, it would create support issues even if it would be trivial to implement. For others, it would create issues since other software would have to be modified to reflect the changes. For others, the software did not have a distinct configuration directory so untangling it would be a major effort.

In the case of the latter, just look at Firefox. Yes, it recently moved the .mozilla directory to .config. It is in no way reflective of the XDG standards. Among other things, there are log files, cache files, and add-ons in there. In my mind, that is worse than having ~/.mozilla. Instead of having a directory that can be cleanly backed up, with the exceptions being elsewhere, I am left having to sort through everything. I don't blame Firefox for taking that approach though: users were demanding a clean home directory and the developers had legacy code to deal with. They simply took the path of least resistance. (That said, Firefox isn't the only culprit here.)