You've move the goalposts a bit here, but for the sake of discussion...
On windows we have Chocolatey available to help with application-level package management, granted you need to install it first but I would argue thats not much different than needing to add a PPA or new apt source before apt can install the right app/version you're looking for..
@powershell -NoProfile -ExecutionPolicy unrestricted -Command "iex ((new-object net.webclient).DownloadString('https://chocolatey.org/install.ps1'))" && SET PATH=%PATH%;%systemdrive%\chocolatey\bin
ugly command, but it works.
Then:
cinst [x]
It isn't perfect but its getting better. No UIs launched, all done via console. Handles adding items to the path, handles portable executables, etc.
NuGet is great, apart from a few issues and has been in that state for quite some time. Not sure why we require things to be good for a decade before we're ready to talk kindly about them without the air quotes.
There are a ton of tools for scripting .NET builds but the real trick is that most people don't need to do anything 'special'.
msbuild Solution.sln or msbuild Project.csproj
Your project files can include any number of pre/post build targets to handle any scenario you can imagine. Again, not perfect but manageable. If this isn't to your liking you can use all the build tools for other languages if you like.. Many people like Rake as a general purpose tool and others have done the work of providing msbuild integration there for you.
Your .csproj file is built for you by Visual Studio (or by hand if you wish) and from there you can add much of what you need for your builds. I have worked on several very very large codebases for enterprise projects and there has never been any serious amount of 'boilerplate' to setup for builds.
What about Continuous Integration and Deployment? Microsoft didn't build one for a while (not sure if they've built one and baked it into TFS) and y'all have to rely on CruiseControl or TeamCity or Bamboo or something else.
For CI, you can use TFS if you wish (really, really easy to do but somewhat limited in its ease of customization), or Jenkins, TeamCity, CC, Bamboo, whatever.. Its the same for any language. Pick a CI tool, install it, use it. Hardly a weakness of one platform over another.
As far as deployment, that depends on the type of application you're building. Could be as easy as a git push that deploys to Azure/AppHarbor or it could by a PowerShell script or possibly a ClickOnce deployment. Any one of these can be triggered from the VS IDE.
I recently interviewed a senior .NET developer who said to me that he deploy his ASP.NET project from VS.NET IDE (like y'know... hitting F5 or something) to the Production server!
Certainly this must be the norm then. Capability to deploy from the IDE is great for testing but the same things are available for scripting to put in a real deployment process.
Let's take it a little bit further: Docker and Vagrant are useful tools for automation testing. Docker doesn't exist in Windows. Preparing Vagrant for Windows require you to have licenses and probably you have to figure out how to script software installation (you could cheat a little bit by preparing a Windows OS + a base software installed). Compare that to Ubuntu on Vagrant: breezy.
Yes, containers are great. Windows doesn't have them in the sense that Linux does with LXC. Vagrant can and does work well on Windows. The licensing situation isn't as you think though for most .NET devs - they are likely working with MSDN provided software which provides licenses. As for scripting installs, again - chocolatey. Vagrant + chef is a win on any platform. I do wish it worked with Hyper-V client services properly though.
At the end of the day: you cannot automate the process of calling a Sales person in order to get the software, which, in the F/OSS world, such workflow doesn't exist.
At the end of the day: people believe what they want to believe. Windows as a platform is incredibly capable. Its not perfect and it can't compete on every level but it is getting better constantly.
I work with Windows daily - using .NET, Node.js, Ruby, Python and more. I also work with Linux daily doing the same things. The biggest issues I encounter have more to do with package developers using non-portable code than anything.