In fairness, MSIX is very different to MSI and ClickOnce was primarily a way to bootstrap MSIs from the web.
MSI (long since deprecated) is essentially an ad-hoc relational database serialized to a file with embedded blobs that tells a generic engine how to install files and update the registry. It was written for Office in the 90s and was therefore dominated by the retail model of physically shipping CDs.
MSIX is a totally different beast. It's more like a package for Linux. The format is a signed zip file with some embedded XML files. One of them is a "block map", which is basically an index into the zip data by chunk hash. Packages are installed to immutable directories, which lets Windows optimize out the download of data it already has on disk by copying from other packages or even just hard linking files together. Delta updates thus come for free (albeit not as powerful as diff based schemes when inserting data into the middle of a file). Another XML file declares how the app should be integrated into the OS. The old MSI/EXE model of manually patching and unpatching the registry and filesystem to do integration is gone here; for example, if you want to register a CLI command then that's an XML tag, if you want a file association or URL handler, that's a bit more XML. Windows takes care of wiring everything up and removing it on uninstall.
Most importantly, MSIX takes care of online updates. MSI never did this. You can register a URL for a package that points to yet another XML file, and Windows will download deltas and apply them in the background even if the app isn't running (a la Chrome).
So Microsoft's packaging tech hasn't churned that much. There were CABs from the Win3.1 days, then later MSI from the late 90s, and starting in Windows 10-ish timeframe MSIX. All of these are very different technologies.
One of the nice things about MSIX is that it's feasible to create them from other platforms, because although Microsoft's tools are Windows specific the format is simple enough to reimplement. Not simple - the way they compute the block map and signature data effectively requires you to write your own ZIP library to create them - but it can be done and that's why the new Conveyor tool [1] is able to create Windows self-updating desktop apps from Linux and macOS. If you have a pre-compiled runtime like Electron or the JVM then you can push out updates with one command from your Mac/Linux dev laptop, it's no harder than publishing a static website by rendering Markdown to HTML, and that makes it feasible to develop quick lightweight desktop apps in a convenient manner. With the old MSI or InstallShield tech it would have been much harder to create a cross platform tool like Conveyor.
[1] https://hydraulic.software/ (it can also do Linux and macOS apps from Windows, but those are a bit easier)