You should probably move this thread to the modding section (as I just tested out the Bacco and he was not dividing my xp).
Take for example the CoS mod. This mod doesn't change any of the units stats but it does make a copy of each of the units in order to add the background stats to them. Hence, this mod will change these core figures, and if your mod is loaded before CoS then your mod will be overwritten by the way FE:LH does unit modding (you have to copy the entire unit and it replaces the original copy).
There are a lot of mods that will do subtle changes to the units, like some of my henchmen mods do some subtle changes and most people do not realize that the mod is incompatible with other mods. When I claim my mods are compatible with CoS, I ensure that my mod is always loaded after CoS if I overwrite some things in that mod.
I can't say what mods you are running that is preventing the changes from happening, but there must be something causing the problem. Or it could come down to how do you know that these heroes are dividing XP? It is not an easy thing to test in general, I tested it by destroying the same group with the SAME combat rated army to ensure the same XP from both fights. Higher combat ratings can also cause lower XP.
From what you described you should get a unit that will not divide battle XP. I don't know all the details of your current mods and how you are changing the files, but as far as I can tell it should tell FE:LH not to divide the battle XP.