The amount of time it takes to process the packaging, and later to install the package is unacceptably high right now. My benchmark for this is the app Anaconda, which compresses to just under 2GB. If the time to install on a given system is X, the time to get through the log processing is about 3X. Time to install the package is also huge. While never that great for App-V packaging either, the sequencer never took that long.
This will register the app with the OS / Shell. You will be able to run the app from Start to ensure it runs properly. Once you have things working, you can then package the MSIX. (Use SDK version 10.0.17763.0+ of makeappx.exe to create the MSIX.)
Don't forget to test the packaged MSIX before deployment.