It seems to be that there should either be a tool that can help with tracking these bonuses during scenario creation. The only viable alternative that would allow local deployments to claim a rightful place among the other features would be to have a second version of all big maps out there.
There is a tool, you can usee to find superbonuses/be used to fix this (for 99%) for all big maps using mods*. You do need a M to use it thru. Since all superbonuses tends to be quite big, this mod can fix it.
*The mod is 'BonusValue QuickOverrider' and is made by me. I also have a unreleased LD helper mod, that gets rid of the tedious work of entering the same orders every turn. Also, since this overrides bonus values, you can save the template after, and remove the mod. Meaning the games will be mod-free after.
Of course you can also make your own mod. In short, this is already in the game since we have a mod framework to use.