I set up the area to be captured on desktop via the www site for DD (I think in PH the area has to be set up in the app - i.e. no desktop option). In the former if going to be outside data coverage range, load up the area to the app before going out. I leave most settings as default - though set the altitude to that mentioned above (which is the maximum legal in my area). Align the flight tracks to be on the long axis of the area to minimise the turns & maximise efficiency. In consideration of the overlap % in the settings & the proposed flight track, expand the area if the edges you want won’t be in at least 2 images.
In addition to those 2 apps, I run DJI Go 4 to check the basic settings such as return to home altitude, compass calibration, etc. I then go over to one of the other 2 apps (am warming towards DD) to fly.
I think your original option to stitch the images together (AgriSoft) & anything similar should work with images captured via any control app as they will all have the x, y, z, tilt, pitch, etc. information required. On my list of things to do is capture via DD app then upload to the PH site to see how that goes.
