2 methods that are not really desirable or worth it:
Uninstall it with rpm-ostree and end up using more storage and slower updates since you are now creating an additional layer to the image to remove Waydroid. No benefits but the Waydroid package will no longer be installed on the system.
Make a custom Bazzite image and remove Waydroid from the image, so you won’t have the downsides mentioned above with slower updates and more disk space, but now you have to maintain a custom Bazzite image that changes one thing. I recommend this option if you feel technical enough for it and want to do more than solely remove the Waydroid package.
I just don’t know why the maintainers of Bazzite would make waydroid an app that can’t be removed. It poses a security risk… have you seen the garbage .apks available?
Because Waydroid isn’t available as Flatpaks, and installing it within a Distrobox adds even more complexities and requires more effort to get up and running, especially when handheld images and gaming mode is taken into consideration. So waydroid is installed as a native package, like Lutris and Steam.
If you’ve never initialized Waydroid, or have ran the reset command and never re-initialized, then Waydroid isn’t functional. You can disable the waydroid-container.service unit for an extra measure if deemed necessary, and then even mask it if you really want to be sure it doesn’t run ever unless manually unmasked.