Here is how I made the adjustments: Take Pedro Martinez in 1999. His ERA+ was 243. That was calculated by comparing it to the league average and adjusting for the run environment of his park.
His ERA that year was 2.07 while the league average was 4.86. 2.07/4.86 = .426. Then we have 1/.426 = 2.3478. The park factor for Fenway that year was 103, meaning pitchers gave up 3% more runs than average there. So 1.03*2.3478 = 2.42. That gets multiplied by 100 (Baseball Reference has him with 243, probably due to rounding differences).
Then I converted that into an ERA in a league whose average is 4.00. I call that ERA* in the table. Martinez would have 1.65. But, that needs to be adjusted based on his FIP ERA (which is an estimate based only on walks, strikeouts and HRs). His FIP ERA that year was 1.39 or .68 lower than his actual ERA of 2.07.
Then I lower his ERA* by .68. That leaves us with 1.65 - .68 = 0.97. And that is the FIPERA* which is the FIPERA relative to the league average and adjusted for park effects.
I listed the top 27 instead of the top 25 because there are two pitchers from this year, Kershaw and Hernandez.
Martinez has 4 of the top 6 seasons, 1999, 2000, 2002, 2003. In 2001 he was hurt an only pitched 116 innings but his FIPERA* is 1.35. He also managed to finish 6th in WAR for pitchers that year.
17 of these seasons have come since 1995. There was only 1 season between 1911 and 1967, Newhouser in 1946. But this is a high strikeout era and FIP ERA takes that into account. Maybe there is a way to first find HRs, walks and strikeouts relative to the league average and then adjust for park affects. Things might come out differently.
Missing from the leaders above are Alexander, Grove, Vance, Hubbell, Feller, Koufax, among others. Here the best FIPERA*s for each of them
Bob Feller 2.63
Dazzy Vance 2.78
Carl Hubbell 2.94
Lefty Grove 2.71
Sandy Koufax 2.45
Pete Alexander 2.38
Alexander's season ranks 41st.
I also did something similar for career FIPERA