So, about the embedding side of things I donāt really know a lot, honestly. Just that Ink is designed to be embedded, and Inform (to my knowledge) not. So I just made the assumption, it would be easier with Ink. But then, they focus mostly on integrations into engines like Godot, Unreal, Unity. Here is, as example, some docs on how to do in unity, but there is also a javascript-port, since you mentioned ECMAScript.
To your question, how much can one shoehorn the one style of IF into the respective other - yes it works, in both directions, to some degree, with some clunkyness involved. I started once doing a parser-based thing in Ink, until I realized the combinatoric explosion of options presented to the player in certain situations. It is a fun experiment, but in the end itās probably better to use the tool suited best.
One element that made me suggest something choice-based, would be dialogues, which are usually implemented in a choice-based manner (pick one of several answers). This is possible in Inform, the question comes up in this forum now and then, there is some plugin available to help with that, from what I read.
With the help of tracking variables, you should be able to track the current state of the mission in Ink, where each system could be a knot (passage), and depending on certain variables, you can change variables in ink, query those in the actual game and depending on the outcome, trigger events.
For example, in system A you have the offer to transport a mysterious passenger to system B. Once you arrive in system B, you could query if the player accepted the offer, and if so, greet him with a fleet of police ships.
Just remembered, this blog post gives maybe some practical insight on how it works (unity-based, again).
And when I talk about Ink all the time, no I donāt get paid for it
Twine is actually the noticable more popular and known contender, I just donāt know too much about the ability to embed it.
Overall, I do like your idea though, and I feel kinda tempted to dig out Oolite again. Last time I tried, my motivation (and ship) shattered a bit too often a few meters next to the station entrance.