National team competitions:
You are confusing the UCL system with UEFA qualifications for the Euro Championships and World Cup, and that will be for playoff berths only. Games against last are only discarded to find out what are the better placed among ALL 2nd placed teams (3rd placed for future Euros) in order to access playoff.
The reason:
Not every group has the same amount of teams.
In the UEFA Champions League and most competitions:
All goals and matches matter all the time and if 2 or 3 teams are tied in the same place (whatever place is), games between them will be analysed in particular. Which is unfair because you might have lost 0-1 against 1st place and won against 4th by 7-0, while overall your friend could have lost 0-7 to the first and won 1-0 against the last, which shows he's much worst than you.
Why it works:
It often favours the worst team, but helps preventing 3rd party teams from fixing matches. You could be tied in point while teams with unknown interests in your dispute could let you score any amount of goals you needed. That's what happened in 1982 between Germany and Austria. Germany only scored the necessary 1-0.