But one thing I always thought should be obligatory was that during installation of such programs, only the resources absent from the system would be added to the installation/system and any other resource bundled would be automatically discarded, thus saving disk space and avoiding redundant libraries present on the system.

Do flatpaks have such working structure?

It’s possible, but rarely allowed because that would produce instability. Linux programs are built to rely on a specific version of a library. Depending on how much actually changes, you can sometimes get away with using a different version than the one it expects, but the more it changes the riskier it gets.

One of the major goals of flatpaks was to create a way for developers to ship one build that was guaranteed to run the same regardless of distro or environment. The isolation is very much the point. It does use more storage space, but in most cases it’s not enough to matter. When storage space is at a premium, yeah, you generally want to avoid containers. They trade space for stability.

Pretty much everything in the Linux space is converging on this concept. Desktop is moving to immutability with flatpak apps. The server space has been entirely taken over by containers. Even Valve has shipped a separate Linux runtime for as long as they’ve officially supported it, and they’re progressing on deeper containerization. You can direct it to run against your native packages instead of the runtime, but it’s rarely a good idea.

The point is that it gives developers a single target that they can all rely on, instead of having to account for 20 distros with multiple still-supported versions each. And believe me, these efforts have made Linux so much easier as a user as well. It used to be that lots developers only targeted Ubuntu. Trying to get anything to run on another system was off like pulling teeth. Now, you can almost always expect to find a flatpak instead which runs on any distro.