I fly my DJI Phantom 4 Pro missions at 300’ above the takeoff point. The 17 acres site drops 140’ at the Eastern boundary so the drone is at 440’ AGL but the trees below stick up 100’ so 340’ above the tree tops. On the Western side, the 100’ trees put the drone 200’ above their tree tops. I set the overlaps at 80%/80% which is based upon 300’ above the takeoff point. So this results in less than 80%/80% overlaps over the Western trees but more than 80%/80% overlaps over the Eastern trees. A reasonable compromise. I get good maps using these settings.
Can you do something like this on your site? Try flying at 300’ which will give you 200’ AGL at the high point of your site but up to 300’ elsewhere. If you set the overlap to 80%/80% which will be based upon the 300’ AGL of the takeoff point, then your overlaps will be similar to mine and you should get good maps. I do not think you need two missions for your site with relatively modest elevation differences like mine. But try it if you like and compare the results. If 300’ leaves some holes in your 2D map, try 350’.
I also recommend flying on overcast days in low wind with the drone max speed limited to 9 mph to avoid noticeable blurring in the photos. I do use automatic focus and exposure. I tried using the DroneDeploy defaults for flight speed but this ruined several missions (very blurry photos) as it did not fully compensate for the overcast conditions. Be sure to review every photo and remove any from the upload that are noticeably blurry. For me this results in the elimination of almost all the photos at the 18 turns in my mission on the 17 acres site. The turning is too fast and it badly blurs all the turn photos. So I end up with about 200 photos to upload which is 11.8 photos per acre.
Another nuance is that the RMSE of the mission may be better if you can fly with the long legs of your mission aligned with either constant latitude (my case with 1200’ long E-W legs) or longitude. This may be what is responsible for the 7X better Y vs X contribution to the overall RMSE in my case.