Hi Johnson,
i think, the content of one document showing up underneath another document in the API is a random event and depends on far more than only the two involved files, but rather the entire selection of open documents. Plus, I have the strong suspicion, that it has something to do with the botching of our CMS' addin upon file operations. So I'd be careful, blaming Autodesk alone for this oddity.
But what I blame Autodesk for 100%ly is the complete mess up of the presentation environment that came along with Inventor 2017 (I think it was 2017 - we jumped from 2016 to 2020)! Dear Lord, what were they thinking?
I finally managed to solve my initial problem, which made me stumble over this API-inconsictency. It just took me almost the entire afternoon, to figure out, what i am doing wrong in this insanely counterintuitive (not so) new (anymore) presentation environment.
And trying to render the original functionality of the presentation Environment unusable and hiding its Objects in the API, (i.e. in the Objects-catalog they're tagged "hidden", and the only way to access them seems to be by querying the BrowserPane-Object - i can't remember if that has been like that ever since) is not helpful!!
I'd bet 90% of all Inventor users feel absolutely no urge to create some foolish animations using the presentation environment. Their main purpose is to create exploded views and put them onto a drawing sheet to create some assembling instructions. And for this purpose, Autodesk has totally busted it! Maybe creating an exploded view from scratch somehow still works halfways, but editing it, especially after changes of the source-assembly, is a nightmare!
So please stop pushing users into something they have absolutely no use for! If some people like it - granted! But please implement an option to put things back to "normal", i.e. behaviour like pre-2017, especially - please, please please! - spare me these obnoxios storyboard-overlay-window, which I have to click away EVERY time I had a glance at the source-Assembly and return to my presentation!