Thanks for the additional information. A picture is worth a thousand words!
The navigation pane that you see on the right-hand edge of the screen is a function of the system PDF viewer - that only appears with multi-page documents. The navigation pane should not (and as illustrated - does not) obscure any elements of the document itself - and should not impact the ability to edit/markup the document.
The Navigation Pane is designed to permit easy navigation of multi-page documents - this being particularly important when using the Markup features of iPadOS with an Apple Pencil. Screen gestures have been seemingly contrived to optimise and disambiguate navigation (with your finger) and drawing (with Pencil).
To my knowledge, it is not possible to hide or otherwise configure the behaviour of this system feature.
I have two suggestions:
1) Identify a third-party App that better meets your needs - in this case, an App that provides document Markup features without the Navigation pane.
2) Submit a feature request to Apple using the product feedback portal:
Feedback - iPad - Apple
I hope this information and insight proves to be helpful - if only, perhaps, in better understanding the features with which you appear to have difficulty.