I fly Lufthansa a lot and I can't say that I've seen any of that. Also, if you checked them as luggage, you have no idea how they were treated once out of your sight.
I was totally allowed to bring my car seats on board myself with Lufthansa. I used to work at Frankfurt Airport and parents did it all the time! The LH personal never touched them.
Also, you don't know if your car seats were really safe. There's no way of telling by just looking at it. No, the Scenera either. If you're in a crash, your car seats are replaced, even if they don't have obvious damage. Same goes for checking them as luggage. Don't kid yourself that it was impossible due to "simplicity" or some other excuse like that. The only way to truly know is if you get into an accident later on... so don't be so sure!
Also, obviously no one said that a baby has to stay in a car seat for the entire flight. That's silly and not a valid "excuse" to fly with a lap baby. When we go to America, it takes 11 1/2 hours. We're up, walking around, etc. But when they drop off, which they have to in that period of time, they were safely strapped into their car seats. Then I could get some sleep too! But when they were awake, they were in my arms. The most dangerous portions of the flight are take-off and landing. There's no way you can hold your child. There's just too much G-force.
Getting car seats through airports wasn't a big deal for us but I was very organized. I also left car seats at my parents for visits so I only had to bring one at a time.
If you want to save money by flying with a lap baby, that's your choice but please don't promote checking car seats as luggage. This is not safe and someone following this poor advice might arrive at the airport and be forced to drive with an unrestrained child. Driving, as you pointed out, is much more dangerous than flying. Also recounting that somehow certain airlines are all careful with car seats is not valid either. I've never seen that and I've been flying out of Germany for ages.
Lufthunsa once lost three of my four suitcases but the car seat was with us so my dd was safe on the 2 hour drive home. We got them back 4 days later.