Yes that’s about the only thing you can do to to account for overlap. One other thing you need to calculate is the efficiency of the zones. That will help you account for the fact that some spots don’t have overlap and is an advanced setting for each zone. The below post includes a link to the pdf I used when I ran my catch cup tests and calculated everything I needed
As far as the area goes, I just divided my area between all my zones so that the sum total would be the actual square footage of my lawn. I thought this would be most accurate to calculate the water delivered but I didn’t think about it too much since as you said it doesn’t actually affect run time.
You should still use flex daily, I don’t think this impacts the savings you would get much. The only annoying thing about it is you have to keep an eye on the scheduled runs to ensure the zones that overlap track each other. I think because of rounding error the zones will eventually start diverging in the moisture calculations even if you have the exact same settings for each zone. Eventually they will start running on separate days which is not ideal. Just today I had to adjust my moisture graphs to sync up my overlapping zones again.