Expansions placed through research have a double penalty both through the research progress penalty and the placement of expansions penalty. You indicated just a few % increase in difficulty. Would 3% make sense?The expansions are irrelevant since they only count if you place them. Even if you do, they'll only make a few percent difference per chapter.
Expansions placed through scouting/provinces would have the single expansion penalty.
Expansions placed with diamond purchases have only 75% of the expansion penalty.
Just after the rule change while sneezing into the flour I placed 6 expansions. I didn't see it coming. The only way I can fight now is to place 4 or 5 fighting boosters at a time. That is when I paused my city progression to advance my AW's.