You probably have far more expertise in this area, but I don't see this as solid evidence that MSFT is walking away from MSI. I mean, they also removed WOW64 and the GUI.
It would be absurd to think that MSFT would ever drop support for the GUI in every version of Windows Server. :)
I don't, my earlier thoughts should indicate that I have less (or none). Thinking about this more it's more likely that Nano Server won't have packages at all: the container will be the package. You'll build the image and it will have whatever it has. If you need to add/remove 'packages' you will build a new image. So, no need for package management inside the container -> no need for MSI.
That's actually a really good thought about the reason for MSI removal in Nano Server!
(And, TBH, my only experience with MSI was briefly working with a vaguely recent version of InstallShield several years ago. The fact that you can talk about the pain of MSI authoring probably indicates that you understand more about the topic than I do. I just clicked some buttons in the InstallShield UI, and skimmed some of the MSI developer docs. :) )
It would be absurd to think that MSFT would ever drop support for the GUI in every version of Windows Server. :)