Interesting work. Just as I was saying in another thread about the NPV, everything tends to balance. Republicans held their majority comfortably despite losing the popular vote in 2012, and it looks like Democrats would be favored to do the same in 2020.
There seems to be a very strong incumbency advantage for House members in presidential years that can result in a large gap between the NPV and seat share. Historically, wave elections have restored equilibrium and have resulted in roughly proportional outcomes.
The electoral college advantage bounces around frequently (Obama had in his favor it both times), and House gerrymandering erodes over a decade, sometimes rapidly. To the extent there is a long term problem, it's in the Senate, where the more rural coalition has historically held onto power for an excessively long time.
*The 1955-95 Democratic US House majority stands out, but it effectively had a 3rd party in its coalition, which was needed for control for all but a few years in the late 1950's/early 1960's and late 1970's.