Think of it like you have a base OS that is stock, like Fedora Silverblue/Kinoite. Then the different ublue offerings, Bluefin/Aurora/Bazzite/Ucore take those and add new things on top. If you rebase, anything you installed as a user isn’t touched. But all of the addons change to whatever the default is for that ublue variant.
So someone rebasing from Bluefin/Aurora to Bazzite will have Lutris and Steam (and other gaming specific software and system tweaks) automatically ‘layered’ as part of the default experience, since Bazzite is targeted primarily at gaming, and the other two for general desktop use.
You’re swapping out the default system image, just like when you update and the update is actually just replacing your entire OS with the new version (until the feature that let’s them only replace things that have changed gets finished).