Brew for native commandline apps, Distrobox for software that runs on other distros. Boxbuddy (GUI) is an easy tool to create and manage distroboxes, and the default terminal app, ptyxis, allows you to switch distros easily from the top-left dropdown.
And more options in the Bazzite docs https://docs.bazzite.gg/Installing_and_Managing_Software/
Flatpak is great for two groups of users: the ones who only use default settings in standalone apps and the privacy-oriented experts who know how to tweak things to their liking. In the middle is a large group of users who don’t know or care how things work, but they want that one feature an app is supposed to do but mysteriously doesn’t work with flatpak.
Even one of these occurrences is enough to make most users give up on that app or the OS entirely. I like the idea of sandboxing apps, and I use flatpak daily, but we have to acknowledge and hopefully improve some of its limitations or many users (yourself included, it seems) will consider it unusable.