Alibaba also provides an OpenSource App, it even has support for their multimodal voice chat Model qwen2.5 omni: https://github.com/alibaba/MNN

No, programs not downloaded with the package manager are also not updated by it. Many Programs, like Firefox and probably Mullvad bring an autoupdate feature that is enabled if they are installed manually. If an update is available you will probably get a notification in the app to restart your browser so that the changes are applied.

Yes but without VSCode wouldnt Atom be like vscode: having many unfree extensions?

How did they crush open source competition?

The MS store is replaced by OpenVSX by the Eclipse Foundation. Some addons are not there. E.g. M$ closed source addons e.g. for remote development over ssh or their python and C# extensions.