Linux

You're right - having multiple copies of everything is a drawback of housing each application in its own container or VM. The standard rejoinder is that disk space is cheap. The validity of that rejoinder depends on what you're doing and what hardware or budget you are working with.

Another problem is that old versions of these dependencies will be baked into an image that is then used for many years without updates. This ensures the application keeps working without being disrupted by an update to a shared library, but it also means things like security flaws persist. Arguably, this is mitigated by only that image having the problem, but one insecure app can be a real problem - especially when it accesses shared resources - and when the same problem applies to many applications.

Compiled code optimized for a specific system's hardware is less relevant than it used to be - even Gentoo users do not focus on this anymore. Rolling your own container isn't much harder than compiling with your own options.

Flatpaks really have the added benefit of things just work. Many distros have problems with codecs for example and need to install extra packages to get video working in Firefox. The flatpak version doesn't require any of this and you can just install and move on with your life. Yes dependencies are "redundant" sometimes but you have the added benefit of a really clean base system without hundreds or thousands of lib or dev packages. Also sometimes you need a specific version of a dependency. Let's say you need to update it for compatibility with a specific package but that breaks another which needs an older version. The system can stay especially clean when it comes to the toolbox utility and dev environments (this is available in other distros as distrobox I think).