Hello! I think either approach that you describe would have its pros and cons, but the biggest thing that stands out to me is one that you mentioned - if there are permanent changes you decide to make then you'd have to make them across all of the maps. Unless there are huge changes between each version (which it doesn't that sound way), I would recommend just having one map and using scripting to make adjustments.
So, I actually think this might be a good situation in which to start building out the scripting system some more. :) It would be great to just go ahead and start implementing those events that you'd need since it would help give me direction of what scripts are useful and you could avoid the need for multiple versions of the map.
Feel free to create a list of scripting functions that you'd like to have available (for example, swapping dialogue), and I will try to start working them in. And if you could sort the list in order of priority, that would be even better. :)