This idea is sort of two parts -
Part 1. First, AGO should mix in its json updates, rather than overwriting. Like if I make some customizations to some properties in AGO-assistant, AGO shouldn't overwrite them when I update that item. It should mixin the properties that it knows or cares about, and leave the rest alone. This would allow developers to add additional properties to webmaps that could be used in applications other than AGO and we wouldn't have to worry about people editing the web map.
The new webmap capabilities in 4.x support's adding actions to a layer's JSON via ago-assistant, but when the popup config is modified in AGO, it overwrites these customizations. (#1 would fix this). BUT long term, it would be nice to have AGO simply support Actions in the popup configuration tools. 4.x supports actions so I would assume that AGO should support them as well.