It is possible, currently, to access the PDF markup mode (so as to generate and save a PDF document) without invoking the Markup tools...
Triggering a screenshot in invokes the Markup tools - active for both “finger” and “pencil” input. Instead, from your open App, select the Share icon at top right, then select Print; this will open a print options screen. Now, with two fingers, pinch-outwards on the document thumbnail; this will open the PDF markup mode without the Markup tools. Save your PDF to the path of your choice.
Does this workaround solve your problem? This doesn’t actually disable the Markup tools - it simply doesn’t present them - and therefore inhibits drawing edits by both finger or your pencil.