Most tools that benefit from your current environment are lacking in flatpak. Basically any IDE is going to feel awful without the proper tools. I can't run c++ in CLion without the proper tools, and good luck installing them.
Dev toolchains are infamous for pulling a ton of stuff into your system, and certain languages make switching versions a pain as well. So you install your IDE and whatever flavour of the month tools you need in a distrobox container, using regular dnf packages, and keep your base system clean. With distrobox you can give those tools a separate $HOME as well, in case they litter your main one with dotfiles and dotfolders.
If you work on a certain project long-term, you can then clone the distrobox and keep it around as-is, to ensure against breaking changes in some of your tools.