Mod requests (orders).

Let me write this a third time: in the mod for all campaigns, there are no changes to the "Suzerain" specialization.
Download the mod for all heroes from the campaigns, remove the mod for all campaigns, and test with it. Did you account for all discount modifiers (expert counterstrike gives 30%, seasoned commander), if any were present, and the note from the manual. Then compare how it works in the original to be sure whether there are discrepancies.

So, I replayed it exactly the same way (didn't take counterstrike or seasoned commander, just like before) on version 1.6 without mods: Isabel at level 12, the cost of upgrading a peasant to an archer is 116 gold, all correct.
It seems that on version 3.1, when porting all campaigns, there is indeed some kind of error.
Moreover, she reliably gives 250 gold to the treasury.
Maybe you or someone else could check this point to understand where the cause lies.