Hough -
The neutralized stats are both park-neutral and run-neutral.
This is the same method proposed by Bill James. It is also the exact same method used by baseball-reference.
You can read all about the neutralization process here:
Neutralized and Converted Statistics - Baseball-Reference.com
It doesn't give you all of the math involved for hitters, but it explains some of the process. The formula and example for the pitchers have a couple of typos too, but you'll get a better idea after reading it.
The neutralized stats in OOTP are the best representation of player abilities you are going to see.
As for the Senators ballpark from 1939-1955, it was a pitcher's park virtualy every season, but perhaps not as extreme as you might think it was. Although Vernon was playing for other teams from 1956-1960, Griffith Stadium was not really a bad HR park...at least in those years.
With 1.000 being average, here are the HR factors for Griffith Stadium 1956-1960:
1956: 1.131
1957: 1.072
1958: 0.995
1959: 0.998
1960: 1.005