I agree with your points for the 90% of software that is pre-packaged and ready to install on your choice of distro. I'm more curious about the remaining 10% of apparently problematic 3rd party software that are 'hard' to install on Linux, and how much work it would take someone knowledgeable to create packages for and compare that with the time someone wastes on Windows with more mundane deployment issues.
Are these really comparable? The time it takes someone knowledgeable to do something difficult vs the time spent on more mundane issues where amount of knowledge doesn't really come into play?
But I see what you are saying. The Microsoft provided Windows software maintenance environment is really far behind every Linux distribution. If you have a network of non-mobile machines that mount root via NFS, the work of the admin to install hard-to-install (because it's not available as a package) software doesn't necessarily even require creating package -- you install it on the root. I did this with some one-off stuff we needed that ended up in /usr/local. Voila, everyone has it. And while we all know this kind of software management (packageless) leads to a "messy" system, it's actually easier to pay off that technical debt because you can spend time later to provide a whole new, cleanly managed environment for your NFS root users WITHOUT causing them any downtime at all to do the upgrade. In a properly managed environment, the apparently problematic 3rd party software is just that: apparently problematic. You do the hard stuff ONCE, and that scales out to X number of machines (mobile or not). With Windows, you keep doing the hardstuff over and over and over because each machine diverges and there are so many things you need to touch during the install, and even things like installation are not nearly as automate-able as they are in Linux.
What would be really interesting (and I care about this not very much since I don't do even small Windows network deployments anymore, nor do I have plans to do so in the future) is some kind of installwatch style system for Windows, that re-packages installed software, installed with setup.exe, into, let's say, RPMs, including {pre,post}-install scripts that modify the registry (this is possible, I've used tools that do registry diffs). You'd have to have a clean master Windows machine to do this properly (easily solvable with virtualization), but it could be the difference between night and day when managing Windows installations compared with Microsoft's massive updates and each vendor's own installation method.