Generally, the team(s) chosen in the first (uppermost) selection list is the team whose data file is to be searched. Non-major opponents will be found, but only in years when the searched team's file has data (i.e., that team is considered 'major' itself).
So, for example, if you choose 'Michigan State vs Michigan' in the head-to-head form, you won't see pre-1918 results because Michigan State (the team whose file is being searched) wasn't considered 'major' prior to then. If you search for 'Michigan vs Michigan State' you'll get more of the all-time series.