I assume setting XDG_CONFIG_HOME will have an effect on any program that look for that environment variable. Not all applications do. The worse case is that a new configuration file is created for a program in .config/ If there is an existing program config n the $HOME directory, it will still be there. It will be down to an individual program as to if it also checks $HOME first, before creating something in XDG_CONFIG_HOME

https://practical.li/blog/posts/adopt-FreeDesktop.org-XDG-standard-for-configuration-files/ shows the experiences I had moving to the XDG standard, which has been very positive in my view