P.S: I know there are legitimate reasons for running something on Windows but for any generic project that shouldn’t be the default at all. Linux is the de facto cloud OS.
I don't believe Microsoft is attached to making Windows the default though. Who knows why it is, maybe because people that use the Wizard are likely playing around and will rather want a Windows system? My guess is they'll switch the default if the percentages shift even more and they see that most that manually set something up will change the default. In the end, they want to sell computing and anything that gets in the way, well, gets in the way.
It's not crazy for them to suggest their own home-made soda first, it's marketing. Because that specialty soda makes them more money and differentiates them from their competitors who are just selling off-the-shelf stuff.
It's not crazy to not want to be a commodity.
If you're trying to serve a mass market? I think it is. Wasting time (yours + the customer's) by making them go through and deny the less common options isn't a good idea if you're aiming for serving as many people as possible as efficiently as possible. This would be very different if it wasn't Azure but some local tech company that sits down with you to talk about what kind of server you need and want, what OS best fits your requirements etc, but that's a very different game from what Microsoft is playing with Azure.
With low/self-service, streamlining the process is the right thing to do. In the end, you have to ask yourself, whether you want to earn a few bucks by also selling a licence to your OS, or whether you want more customers. Of course, it's not an actual issue in this case, because you'll usually not manually provision (but then again: why do it if you don't expect to make money by doing it?)
You can argue all you want about what they “should” be doing but they wouldn’t be doing it if it didn’t work.
https://puppet.com/use-cases/windows-infrastructure-automati...
https://www.ansible.com/integrations/infrastructure/windows
There's also Desired State Configuration
https://docs.microsoft.com/en-us/powershell/scripting/dsc/ov...
There's also Group Policy.
https://en.wikipedia.org/wiki/Group_Policy
There's probably a thousand different ways to automatically deploy and manage Windows servers. Its been a thing since at least NT.