apt is not misleadingly advertised as a sandboxing environment. Flatpack is:
"Flatpak: Linux application sandboxing and distribution framework " [0]
"It is advertised as offering a sandbox environment in which users can run application software in isolation from the rest of the system." [1]
The whole point of a sandboxing environment is that you can run applications that do not want to be sandboxed. The flatpack proposition is directly contradictory with this basic requirement, in that it requires the application to be flatpacked to begin with.
[0] https://github.com/flatpak/flatpak
[1] https://en.wikipedia.org/wiki/Flatpak