He mentions that Microsoft had a program where they partnered with large enterprises to collect usage data from corporate desktops. But those computers were on a network even if though often not on the Internet yet.

Stats that would show Doom towering over Windows 3.1 must have been collected manually, maybe by sending people a floppy that contained a program to collect the data, and asking them to mail it back in. "Insert floppy, then type A:\SPY.EXE in your DOS prompt" ...