Why would those runtimes be particularly large? I'd expect the Win32 runtime to be large, but the others should be tiny by late 90s standards. Also, I remember that Windows didn't embed that many drivers itself, but that it had a stable ABI that hardware vendors could target (I remember driver CDs). Further, while the Linux kernel is certainly smaller than all of Windows, my point of comparison was compiling an entire desktop Linux system, which also included a full set of compilers, a desktop environment like KDE, office suites, multiple browsers, etc. Someone working on Windows 2000 shouldn't have to compile all that stuff.

My main question is also not so much why compilation of Windows should be time consuming, but why it should be difficult.