With a 200 parts craft i get as low as 8 fps on Kerbin ascent once i overpass 300 ms^2 (at not more than 5000 m) at any part of the athmosphere. Until i reach FULL orbit, this performance problem will persist no matter the lenght of the trajectory.
Keep in mind that i was doing a really vertical ascent to left the athmosfere as quickly as possible with a overpowered craft. It was not a big spaceplane making a long air breathing ascent.
Coudn't test the reentry because it took too long to orbit and didn't have time left.
Oh, and i didnt report performance problems when the changes were implemented... because i haven't played in a lot of time..