The solution is to use the Javascript SDK. Even if the export was easier to modify, it would still involve the whole C2 engine and require C2 knowledge to work with, and basically be identical to a post-export Javascript SDK. It's better just to write a plugin and modify the capx. In fact, sending the capx as the "source" instead of the exported file is logical, since they can then make arbitrary modifications easily from C2 and re-export if they wish.
The export is actually deliberately difficult to work with because many users are very concerned about reverse engineering. As far as I am aware there have been no cases of exported projects usefully reverse-engineered to Construct 2 projects, so I think that works pretty well and is an important feature.