The flexible difficulty was originally created for Fall From Heaven; pretty novel concept really. Unfortunately in practice it doesn't seem to make much of a difference (Otherwise those options would have been ported over to the RevDCM core).
To answer the OP's question, you can sort of do this with world builder. Save the game in world builder, open the WBsave with notepade, and change the difficulty in the text file (World Builder Saves are text files). As noted though, it probably wol't make much of a difference. Once you are in the later stages of the game and dominating the AI the diety bonuses aren't really enough to make the AI catch up.