With the exception of snaps running on Ubuntu and Solus, snap confinement is limited. Snaps rely heavily on Ubuntu's specific flavor of AppArmor to be able to offer full confinement, currently. Solus imports these changes into their kernel, though I don't trust the changes much because they haven't undergone formal review and have been approved by the kernel developers.
So, for example, on Fedora, Debian, CentOS, or openSUSE, snaps run in "devmode" because of the missing functionality. There's been some work over the last couple of years to upstream some of the work on AppArmor (so openSUSE may partially work in the future). There's a desire to support SELinux properly, but to date, no work has been done. There is an SELinux policy that attempts to confine snapd itself, which was contributed by the guy working on the Fedora/CentOS package for snapd (though it looks like the policy would also work for openSUSE and Debian SELinux setups, too).
Based on conversations I've had with the Snappy team before, it comes down to two things:
* Canonical doesn't know how to work with SELinux at all, and doesn't want to learn how to
* Canonical's customers haven't demanded it of them yet
I find the latter point especially strange given the constant demand for official Snappy support on CentOS and Amazon Linux 2 (which is currently not available yet). Both distributions have SELinux and rely on it for security.
In addition, the majority of snaps are not sandboxed at all anyway, as they operate in "classic" confinement. That is, they're not confined, and have full access to the system, they just use snapd as the delivery system for the software. So even if Snappy confinement actually worked on all Linux distributions, it doesn't matter because most apps delivered through Snappy are entirely unconfined.
Finally, Canonical is the sole arbiter of snaps. You cannot use your own store with it, as snapd is hardwired to Canonical's store. They own all the namespaces, and are the sole publisher. And yet, they have a confusing policy of how they don't consider themselves the distributor of software when they are... It's strange. But because you can't run your own store, you're at their mercy for snap names, available functionality, and so on.
Flatpak, in contrast, is designed to offer the fullest confinement possible with common security features in the mainline Linux kernel that all major distributions offer. Applications register what they need in their manifests, and the Flatpak system handles granting access as appropriate. Flatpak relies on federation through "portals" for interacting with the host environment, and that allows for the applications to have far less direct access than they would normally have. It's basically an Android-like setup, and it seems to work well, though it's still far too coarse for some kinds of applications.
Flatpak lets you run your own repository, so you can implement whatever means you'd like for delivering them, even keyed paywall locations, so that customers who pay get their own access to their own purchases. But most apps probably should be pushed to Flathub, especially if they're free. I think no one has figured out yet how to do paid stuff.
(Disclaimer: I'm a Linux app developer that grudgingly deals with both formats. I'd rather just keep using RPMs myself, as it works well and is reasonably portable.)