Think of it like this: Rpm-ostree layers the stuff you install on top of the base Bazzite image, so it will always need to be re-added on any update. If you have many packages installed this way, it will take a significant amount of time to do so, and also potentially take away from the stability of the system.
By using distrobox and flatpaks for as much software as you possibly can, you effectively isolate it from the image and so it won't interfere with anything.
There's a few things I layer that wouldn't function well in a distrobox - think VPN software, system-wide libraries and APIs, VMs, etc.