Applications such as VLC and GIMP which 'ship' with access to whole filesystem permission is an eternal dilemma. Would you rather the authors ship without access to this permission and break app functionality ? Or let them ship with restrictive permission and allow users to manually enable respective permissions to regain function when the software breaks? It is easy to see the feasible decision here that works for all parties here. The permission on the different accessibility store however has confusing labels on sandboxing, I agree with the point that the store should make this as clear as possible.
I think the bigger point the article misses is the ability to control these permissions at this level. Even if the software author ships 'dangerous' default permissions, the user can always revert this decision and sandbox it effectively if they so wish.
Flatpak is a crucial needed fix for the Linux package distribution problems highlighted elaborately by this article but in my humble assessment, the benefits to this solution massively outweigh the nuances such as the one the author mentioned about package sizes.