Well, the core issue that you're explaining -- the phrase text in the editor when loaded only via an overlay -- is simply related to inline JS vs xfActivate trigger order, which I've changed. If inline JS is not used (and in this case, it's only used for editor phrases), there won't be any change in behavior.
I'm not really stating anything about using inline script. If you have JS B that must run after A is loaded, you may need to look at ways to either change that or change how dependencies are loaded (not using the standard ExtLoader system). When we load external dependencies, we load them in parallel to be faster, so the execution order is indeterminate.