Well that sucks. There most be some code that reverts the difficulty that I didn't notice. I rarely get the time to actually playtest my changes for very long these days. The next time I look at the code maybe I can find it.
I hope you do manage to at least find some time to just enjoy the game!
In the meantime, I can confirm that explorer research is not affected by the difficulty level: I tested 2 same setting new games, prewarp start (to have nothing that would interfere), only difference was the difficulty, from Normal to Extreme.
In each game, I placed 10 science explorers (the same design, saved), manually set them all to research the same initial tech in each category: Enhanced Beam Weapons (standard tech cost), Adv Fission Reactors (x2 cost), and Colonization (x8 cost).
Also, in the research screens no techs were selected to research "normally", so that any research would be done by the explorers only.
In both tests, the techs were completed in almost the same month, with a +/- 1 month difference due to, I think, the time needed to gather the initial scientific data points for each explorer.