Points: 26,754
Rank: UC2 Brainery Advanced Brown Belt
How about this as another idea @vince ? When you get to a point where it would be useful to fill against a markup print the file to a new PDF as @troydegroot suggested and save it as another name. This would allow you to maintain your “live” un-flattened file. Perform the dynamic fill that you are looking to capture, copy the markup and then use “paste-in-place” to bring that markup back into your live file.
This certainly isn’t a perfect approach – it’s kinda clunky – but if you are working with a significant number of irregular shapes it may be faster than re-tracing the boundaries of the area that you are trying to capture.