HusserlTW, after you create the hybrid startpos (following your instructions), you have to delete the second set of \CAMPAIGN_SAVE_GAME\CAMPAIGN_ENV\CAMPAIGN_MODEL\WORLD\FACTION_ARRAY\FACTION_ARRAY\FACTION\CAMPAIGN_BONUS_VALUES (the whole thing), then copy the identical bit from the original startpos.esf and paste over to your new file. This has to be done for every single faction.
Otherwise, you'll get strange bonuses and such from anything you've given the AI in your campaign_difficulty_handicap_effects table, which is suddenly applied to the player when he loads up a new game.