Guessing that USDoD still considered SHIELD to have been "theirs" considering where that committee hearing interrogating Natasha was decorated as being located...?
In think that has more to do with what went down on their turf (the U.S. in general and DC especially) than any part of Shield being "theirs". It's been fairly well implied that Shield wasn't a solely US government agency, but and international one. Like th CIA/MI6 version of InterPol....only with ridiculously advanced technology.
As for the Triskellion, I think Marvel had said some time prior to TWS that in the MCU, Shield's existence was never a secret, but what they got up to was highly classified.
Think of it this way; everyone knows that MI6 exists and even where the SIS building is (you can hardly miss it!) but they don't generally advertise what they get up to on a day-to-day basis.
Or perhaps a more apt comparison, most people have probably heard of InterPol, but only have a general sense of what they're about and probably couldn't name where they're head-quartered (Lyon, incidentally. I had to look it up!)
Eh, for much of their lives, they didn't know who their father was. They grew up in eastern Europe far from him. They can be cryptic about their abilities and origins without deviating at all from their actual origin story. They don't have to use any words that start with M to do that.
Yes, we should remember that Quicksilver and the Scarlet Witch were appearing in Marvel Comics for
nearly twenty years before they were retconned to be Magneto's children. So it's not like you can't tell AVENGERS stories about them without mentioning their parents . . .
Marvel did it for years and years!
This is what only have a passing familiarity with Marvel gets me. I had no idea it was a retcon.
Could Marvel studios get away with having someone say something like, "As far as I know, he was some nobody who died in a car accident. What was his name again? Eh...Ehr...something like that?"
In theory, sure they *could* allude to mutants and Magneto without specifically naming them, but I don't think they *want* to do that. If what's going down the Fantastic Four is any indication, they're looking to avoid even tangentially supporting what's owned by another studio, provided they can do so without loosing themselves a massive amount of money.
Of course it's all supposition based on assumptions and theories at this point. We don't know yet if "the twins" were created by Hydra (with or without the staff---whether or not the staff's gem is an infinity stone or otherwise) or if their abilities are natural (for lack of a better term) and Hydra simply found and recruited/abducted them at a young age. As indeed they attempted to do with Skye.