If I understand it correctly, layering an application is no more dangerous than a regular install on a non atomic os.
True~ish.
There’s an important caveat though; for whatever reason, rpm-ostree can outright fail to upgrade (due to conflicts related to layered packages) while an issue like that is more rare on traditional Fedora and dnf. Thankfully, I’ve never had a problem that I couldn’t solve with rpm-ostree reset run on a (previously) pinned deployment (through sudo ostree admin pin <insert number>). However, when used irresponsibly, this (i.e. layering) can outright destroy your otherwise very robust ‘immutable’ distro.
It’s easier to teach people to be cautious than to teach how they should act accordingly. Hence, uBlue’s documentation tends to be more conservative in order to protect (especially newer) users from shooting themselves in the foot.