Overlaying packages is fully supported with rpm-ostree. It’s a trade off whether or not to use it instead of using a toolbox.
With rpm-ostree, updates are atomic. They either happen or don’t at all. The more packages you overlay, the more likely you might run into a conflict during the preparation for an update, especially if you replace RPMs or use RPMs from external sources or coprs. But your system will always be in a usable & stable state an any time and you will have all the time you need to figure out what’s blocking the update.