But with respect to "Linux on the Desktop" in the context of marketshare, the interest is in seeing how far Linux has gone, not how far software running on Linux has gone.

The only reason "ChromeOS" isn't considered Linux in this dataset is because Chrome has a flag that removes Linux from the user-agent on certain systems. If we were talking about Linux on the desktop casually, or were compiling a dataset through some other means where the kernel is a known quantity, we'd most certainly include said systems.