Can you make custom scenarios use different proto.xml files?

I just recently started playing around with modifying units by editing the proto(x).xml file.

However I'm editing the proto2.8.xml (AOM:EE) which means if I were to play a standard game it will be affected by any potential changes I've made (and online play is probably impossible).

At the moment I've just got a backup of the original file and rename them back and forth, but it's pretty inconvenient.

Ideally I'd want to just be able to have a new proto.xml file in the Data folder which would only be used by my custom scenarion/campaign without affecting normal gameplay.

I've read online that the AoM campaign uses the data from the first proto.xml (and you can see while playing campaign that unit stats and costs are different from current balance), so it should be possible, but I haven't found anywhere in the Map/Scenario Editor to change this.

p.s. I'm currently using Enhanced Edition but if I have to I wouldn't mind The Titans. I already read that if you want to make new custom civilizations and gods you can't use Enhanced Edition so I've already been thinking about switching.