Have things changed since then?
The "sandboxed" icon issue is not even flatpak, but Gnome Software which is NOT flatpak, which makes me doubt about some other parts of this article as well.
My take on Flatpak is that it's still very much work in progress but does go on the right direction. The core issue is that it's not popular enough to be considered as an official way to package software and a lot of it is packaged by Redhat developers or the community. Which means that a package can be easily abandoned, or modifications in the software itself that would allow proper sandboxing are not happening.
Firejail from the above comments seems to handle this quite well with virtual homes.
It is definitely a source of general frustration, and I think largely because people are still often using it for CLI tools rather than GUI tools which can make use of portals to grant file access permission and/or use an arbitrary path more easily - which is how it works so seamlessly on macOS [and is supported by flatpak/snap for GTK3 at least].
(Disclaimer: I work at Canonical/Ubuntu in the Support organisation. But not directly with/on snaps, this is a user perspective.)