Pricing isn't something you can just ignore. Anyone can get started with a free LEMP stack in a few minutes. Windows Server starts at $500 and goes up from there, and you have to pay more the more instances you have. If you start with it, you get locked into it, and it can get very expensive at enterprise scale.
Some enterprises still use Windows Server, especially if the rest of their stack is Microsoft and they can negotiate a bundled license with everything they need. But web startups typically want to avoid the Microsoft tax. Their apps' business value tends to be at the level of a webpage anyway, so the underlying stack doesn't matter as much – it's not like Windows Server gives them any significant advantages over spinning up a standard VM or some managed databases and CDNs, etc. Windows doesn't do anything especially worthwhile to justify that additional cost unless you're an all-Microsoft shop. And these days, when you're typically deploying to web + apps, Microsoft matters even less. .NET is popular in Europe, but in the US it's generally Electron or React Native, etc.
As for external packages, it's a philosophical/historical difference. Microsoft has traditionally favored first-party monoliths (the "kitchen sink" approach) that they can sell as a whole solution at a high price. GNU/Linux is traditionally clobbered together from a bunch of small free utilities, each with different authors, and each managing only their own little sphere of concern. It favors modular utilities that can be piped together or little daemons that run on their own ports. It allows very fast iterations (since any one tool can be reinvented and modularly replaced), but yes, it isn't as batteries-included as a Microsoft stack.
But at the end of the day, free matters a LOT. Microsoft is perfectly capable of making/acquiring popular tools as long as they're free, like VSCode or Github.
You could argue for or against the technical merits of the FOSS model (security, multi vendor support, modularity, extensibility, etc.) but those are minor. Its biggest selling point is that it's free. That's why all the other paid server software of the 90s and 2000s died out too. LEMP is good enough.
I'm not sure what you mean by "server footprint", but I doubt most Linux installs are phoning home in a way that a third party like Statista can easily measure. Unless they provide some detailed methodology, I'd be very skeptical of those numbers.