I had the assumption that the KDE file indexing program baloo was exceptionally slow on Atomic Fedora.
But as it only searches in the user home (symlinked from /var/home/$USER) and ignores all dotfiles, there should be no conflicts with flatpaks, distrobox/toolbox containers, ostree deployments etc.
Unless Fedora does something specific in the KDE configuration, yes: I’ve never seen baloo index folders outside home. But I never tried KDE in Fedora. I use KDE in Arch.