I think the industry has "moved past this" because for SaaS platforms, it takes a lot less labor to enforce sandboxing in-house applications on the cloud than to maintain dependencies across the shop. However, for an OS distribution to end users devices, where applications inevitably ask for an are granted MUCH more permissions than they need, this is not a safe model. It is CLEARLY superior for users and for operating system maintainers, or others responsible for user security, to update dependencies using the traditional dynamically linked model. No work needs to be done to consider the compilation tooling of each individual application.
The existence of Flatpak etc. is a misguided concession from the FOSS community to private businesses and to software developers who are used to packaging for the cloud. The model is not appropriate for desktop or mobile software -- there is a reason that filesystem access is extremely restricted or impossible on mobile platforms, and that even Android has moved to dynamically prompting for permissions when apps use them rather than bundling them into a single prompt at installation.
For Flatpak to work, we need MUCH heavier sandboxing, which will be detriment to productivity for desktop users for certain classes of applications, and may prevent many types of applications from being packageable as Flatpak. I think this is a fine compromise. I'm OK with installing Spotify as a Flatpak (given better security, not now) but keeping my webserver, database, file manager, terminal, programming language, and other "system" software in the OS repository.