I can't tell you how many times people go into a pdf or session and apply a bunch of temporary markings for their own use, discuss options during a meeting, etc. and then those temporary markups end up accidentally going out in a submittal or must go through a formal comment reconciliation process (each and every one…).
How about a view mode that acts like old-school tracing; where you would grab some onion paper or a lightbox and clean sheet to draw over a set of plans without marking the original.
In this mode, you would turn it on like the full screen or presentation mode, and a banner would proclaim that tracing mode is on and markups are temporary (or something to that effect). Include 2 toggles that would show/dim/hide comments or background. Then the user could navigate, markup and measure as normal. At any point the user could select a markup and choose to apply it, and when they close the mode a dialog will ask if the user wants to apply the markups or discard them. Then it would go back to normal mode. The markups list in this mode could show the tracing markups in the list as blue or something to indicate temporary tracing comments as opposed to other markups on the drawing. You would not be able to make modifications to the base pdf while in this mode.