How much of that 60% is running .NET apps, though?
Not everyone who uses Azure is a "Microsoft shop", in terms of programming tech stack. Plenty of people use Azure as a cross-cloud redundancy play, or because they do business with Amazon competitors that refuse to have their data on AWS.
My understanding is that a growing percentage of that is .NET. Even "big corporate" realizes .NET Linux deployments on Azure are cheaper and are trying to cost-cut/cost-save. There's still a small feature parity difference in Azure between Linux and Windows servers, primarily in my experience in "no touch" Application Insights telemetry/logging for application state (and user) monitoring as a major one. If that feature gap closed I expect that 40% to drop rapidly in Azure simply for cost cutting reasons. Anecdotally, I've been feeling internal pressure in my company to move .NET deployments to Linux servers for cost savings and we've done some initial trial balloons on the engineering effort for working around that feature gap.
I met a guy a while back who did stints for both Amazon and Azure orgs.
It's the reverse in AWS, they have a bit more Windows market share than Linux. And he also backed up your statement.
His take (which was just his speculation) was that the virtualization stacks ran those OS's more efficiently. HyperV with Linux VM's and KVM with Windows VM's. I have no idea if that's true or not.
Not everyone who uses Azure is a "Microsoft shop", in terms of programming tech stack. Plenty of people use Azure as a cross-cloud redundancy play, or because they do business with Amazon competitors that refuse to have their data on AWS.