Take Firefox on the latest Ubuntu for example, it installs as a Snap. Unlike the APT package (or any other package manager) version, the usual ~/.mozilla/ directory changed location. This broke some of my customization scripts and other people's scripts I'm using such as https://github.com/black7375/Firefox-UI-Fix
I would really, really, like if both Flatpaks and Snaps could keep the usual program's config directories. Then I would likely use them often because they have big advantages (especially Flatpaks) over package managers, especially for dependencies.