The rules are like that but the problem is how much do people follow/understand the rules... I live in Europe long enough to know this is not the case unfortunately. If it was me, I'd get the visa for the first port of entry because: 1) it is crystal clear to the check-in people, my ticket is going to Germany and I have a visa to enter Germany, and 2) They don't check passport much for intra-Schengen flights - even if they check, the check-in person/gate agent won't know/care how many days you have been this country and how long you'll be in the next country - their job is to herd people onto the plane.