I would really consider re-writing the help for these two options. It's impossible to draw a difference from the help descriptions.
Ignore Areas Ignore Areas are ranges of stations between which volume quantities are not calculated and not included in reports. End areas continue to be calculated for each cross section, but volume calculations are not performed between user specified station ranges. One area of application for Ignore Areas would be bridge overpasses.
"and not included in reports" is the difference. Other wise its verbatum.