I never modded JA2 so I didn't know they used XML/JSON, I was referring to games now. Assuming this is true, it's funny that all these years later games are using the same methods.
It's true that there are mods that change the code what you call, "cheats" or I often call, "hacks" but not all or even most of them. That isn't really, "modding" the game in a true sense but was often the only way to mod games in the past. Go look at Nexus mods or Steam workshop and you'll see most mods are just changing settings in files which can be altered with a text editor. Games today are made this way so that you can have multiple mods installed at once. If they required recompiling of the executable or dll file then you could only have that one, "mod"
I don't want to go further down the rabbit hole of only talking about these hack type mods since the devs have apparently stated they will allowing modding. This tells me there with be things easily accessible to change like the variables I mentioned before. Now I hope we get more info on what sorts of mechanics, art, and data values we can change plus what format these structures will be in.