... pretty much what you said, yeah. It's also possible that the "not noticing" is either simple self-preservation or the result of you pulling some strings behind the scenes. Btw - once you recover the Ziggurat, there are a number of core world encounters that are basically what you describe - so I at least at this point, the Ziggurat is a bridge too far when it comes to being ignored, while the other stuff isn't.
See, I always interpreted the Ziggurat a bit differently. It's so far outside the box that nobody knows what it is or what to make of it, so it's at least plausible that their response is some kind of indignant confusion rather than outright hostility (and also the Tri-Tachs have tried to kill you for poking around their business at least a couple times by then). At a more basic level, even if the hull itself is an unsettling morass of alien nightmares, it's at least being piloted by a human that you can talk to.
Conversely, even if their existence isn't publicly acknowledged, there have been multiple wars fought against them, so there has to be people on various naval commands across the core worlds who know
exactly what a Remnant warship is, know what operates one, and have some very pointed questions about exactly what you think you're doing with one (and don't you try to say you put a limiter on it because
they said that the last two times too).