Yes, for Linux it‘s like this typically (varies by distro):

• Discover (App Store) has two versions of the same application: repository and flatpack
• The website of the project might offer specific instructions or packages for a handful of distros, maybe a extra repository, maybe an appimage

Figuring out the best way to install the software often involves at least comparing two versions and deciding, which one you want.

macOS has many ways to install, but most software only choose one or two. And you usually get the same version regardless of install path.

For Linux you have several options to install and you don’t end up with the same version.