Good, I think I understand better now. And I am sure that you deal very carefully with those things.
I found a workaround that is quite satisfying for my purposes. I created a PDF document that contains a hyperlink to MD (and also other apps) which I open with iBooks. In MD I made a button with the link to iBooks (iBooks://).
Now I can access the PDF at any time (when not in MD) as side-app / slide-over, tab on the link for MD, and it switches immediately to the app.
Or, what's more important for me, when MD is currently the side-app, I tab on the button for iBooks (in MD), then link to MD to have the full page. Ok, that needs two tabs, but is still very fast.
Unfortunately all other apps that I use don't support slide-over or split view, so I always have only this small side window that cannot be expanded. In some situations perfect, but sometimes I desire the full page.
I know, this is a bit stupid, but it works quite well for me. Maybe other users have the same 'problem' and have better ideas than me.