In the pdf and info file, the columns are spaced out nicely according to the prototype. If the prototype is made wider, then the columns are wider. But this doesn't happen in the html output. The width of each column is pretty much fixed to the entry with the widest element.
But if I replace the prototype with @columnfractions, everything works nicely in info, pdf, and html.
The prototype form is much easier to use; it's hard to know a priori what column fractions to use to make the columns spaced nicely.
I tested this with texinfo 6.8 and 7.0.1; they both have the same html column problem.