The blog post answers your question directly:

> For example, you might install network drivers to support your Windows programs. You might choose this option instead of installing them globally because you don’t care about networking for your MS-DOS programs and want to free up conventional memory for them. Or because those drivers don’t support running in multiple virtual machines, so you’ll take them in the System VM and forego them for your MS-DOS programs.

In the Windows 95 era, it was not uncommon to still rely on MS-DOS TSRs for important functionality. Raymond has explained elsewhere about how Windows, after “sucking the brains out of MS-DOS,” maintained the ability to call into these TSRs.