It makes no sense that you could magically fly your flamer in the air and hit multiple levels, nor can you flame through the floor. With these ignore cover weapons, this is a much better rule. As for the fluff of the flamer, if you shoot it straight in the air, why would it fly around, or if you angle it through a floor why would it magically go through a bunch of seams in the floor and pop out on the other side. I think the intent is absolutely to allow some protection from flamers by positioning yourself on multiple levels and force the flamer to get in the right position to flame people. Additionally, the no escape rule would not work in ruins as they are not enclosed like a vehicle. But the flames would roll around any obstacles within the template area. I guess you could decide to count ruins as a building for the purposes of templates and just do the d6 wounds. Like you said, you can't have the best of both worlds.
I have a related but different question. With the no escape rule, would a models in a vehicle on the roof of a building or ruins be subjected to the d6 hits?