Some domains are up there because they're being used by applications, for exemple no one goes directly to microsoft.com but Windows does it for many things like update, monitoring, telemetry ect ...
*.mozilla.org is probably resolved when you use Firefox.
Cloudflare can't know if the resolve was made by a user or by internal application logic.
I imagine microsoft.com received quite a bit of direct traffic last Tuesday when preorders opened for the next Xbox consoles. Also, .NET Framework, .NET Core, Entity Framework, Entity Framework Core, and Azure documentation is all hosted at microsoft.com (to name just a few).
I don't mean to discredit your main point, that a lot of domain use can be credited to application or OS logic, but to say no one goes to microsoft.com is a bit weird.
Edge and IE are still a decent chunk of desktop traffic as well. And opening them with home page will probably kick off traffic to microsoft.com as well. Not sure how much that will be, but probably factors in.
Edit: Although their metrics have the browser share lower than others. They have Edge at <4% and IE doesn't register in top 10. Whereas something like https://netmarketshare.com/ has Edge at 7% and IE 5%. So there is seemingly a bias towards other browsers in their methods. Which makes sense, seems unlikely someone uses 1.1.1.1 and IE.
*.mozilla.org is probably resolved when you use Firefox.
Cloudflare can't know if the resolve was made by a user or by internal application logic.