I never understood the giant focus on side windows. If you want to see your components while you're using your PC, why not just build inside a transparent case, or build on a workbench/open style (caseless)
If you have negative pressure you'll be sucking in air through the gaps and that air won't go through a filter, hence more dust.
Is this really part of the ATX spec though? Or just something people have learned to do for modern cases with air filters?