UPDATE
I took your suggestions to heart and updated the website to reflect the changes I implemented today. The big change is that I found a way to keep pacman fully intact and functioning, but make it apply the changes atomically. So now this isn't just limited to Flatpaks, but LITERALLY Arch Linux but made atomic.
The new intro reads:
"Plutonium-239 is Arch Linux, made atomic. It combines the rolling release model of Arch Linux with an atomically updated root filesystem inspired by SteamOS on top of the heavily optimized CachyOS performance kernel. Unlike immutable distributions that lock you out of the native package manager and force you into sandboxes, Pu-239 keeps the core Arch experience intact. You still get the full power of pacman and the official Arch repositories, with the peace of mind of an unbreakable safety net underneath."
For more information, please check out the updated "How it works" section. Thank you all a lot for the feedback!