Right for the wrong reasons
I am a scientist/software-developer working for a company that sells software to scientists. Linux is our main development platform, and indeed most of our income comes from HPC apps that run on large clusters or GPU-enabled machines, including some on the cloud. Front end-end GUIs run on Linux, Mac and Windows (and, to some extent, in OS-agnostic browsers).
First, the idea that if you build on Linux it just runs on Mac is completely wrong. The back end is easier to port to Mac than Windows because of the shared *x heritage, but easier ≠ easy. Front-end cross-platform compatibility is made easier by our use of Qt, but on this level, it's actually a little bit easier to port Linux to Windows than Mac, because Linux and Windows share the paradigm of separate menu bars for each app, whereas Mac has "one true menu bar."
Though most of us internally have Linux on the desktop, most of us use Mac on our personal machines, including (a) developers developing and testing code at home and (b) field engineers demonstrating SW and helping customers on site.
This is in contrast to our commercial customers, 90% of whom use Windows. So (1) why do our field engineers use Macs, and (2) why do our commercial customers use Windows?
1. Our people use Macs because: (a) We can run Windows and Linux on VMs. You can't run a Mac VM on another platform. So we can support all three of our platforms from the same machine. (b) We do find the Mac easier to use (especially because many of us come from Linux/HPC backgrounds) and also because of the generally acknowledged convenience factors you mentioned. Because of this, our Systems group has to support Mac whether they like it or not; and indeed, many of our customers, especially in the academic world, use Mac. But again, our bread-and-butter is HPC apps that run on Linux clusters, including GPU-enabled clusters, and on Linux on the Cloud.
2. Our commercial customers use Windows primarily because that's what their IT department supports. But that begs the question, why is that? (a) Yes, there is a heritage of Windows support and a large body of Windows-trained system personnel out there to hire. It's hard to find IT admins who know Linux and Mac well, especially when the Linux side includes GPU-equipped boxes, large clusters and the cloud. And there is a large body of legacy enterprise-level desktop clients that run only on Windows. But (b), having been personally involved in efforts to support Windows HPC (which succeeded technically, but not economically), and who has had Windows on my desktop over periods of many years, and who has listened to my sysadms, the fact is that Apple has nothing to compete with the support that Windows has for enterprise-wide management of machine and software configurations. In an earlier post you gave a few alternatives for this sort of support, but, as you concluded, the extent of it does not compare with what is available for Windows.
The fact is that Apple has never really been interested in pursuing the enterprise market and creating such tools. They may never. In the meantime, the past few Mac OS X releases (Mavericks, Yosemite) have been rather unstable, and we are hearing more and more good things about Windows-10. So we could possibly see a reversal of preference, where even people like me decide that Windows makes more sense. But, to be honest, that would be a long time coming.