Because, the team standings of course, i.m.o., have to represent the best teams in the tour. In your way the best team could possibly be the team with the worst general classification times at the end.
On the other hand, in the current system you might not be the best team if 3 of your riders really suck in their secondaries (and for example every stages two of them fall), while the other two always end up in the first group.
I don't have a good alternative yet, but I suppose you're right if you say that this system of team standings isn't totally right.
Zatarra Pro Cycling Season 2: Division 5:54 3rd Season 3: Division 4:58