Hi jamiesbrain,
There are a number of apps already available which help you with flight planning for UAVs from DJI:
1. MapPilot
2. FlyLitchi
3. DJI GS PRO
Acquire images using one of these apps and then simply import them into PhotoScan Pro. Location and even orientation (if enabled in Tools>Preferences>Advanced>Load camera orientation angles from XMP meta data) for each photograph are automatically imported and the coordinate system is automatically set to WGS84.
Not sure about the benefit I would get from a PhotoScan flight planning app. In case of Pix4Dcapture, Skycatch or Dronedeploy you get cloud processing, but that's not an option with PhotoScan (unless you set up your own 'PhotoScan cloud').
You can already export all files from Agisoft in a format that is readable for any GIS software (e.g., GlobalMapper, ArcGis, QGIS, ...). Simply use batch processing for that and export for example the DEM and orthophotograph as geotiff to the same folder. Alternatively, you can use Python Scripting to further customize your processing workflow or to even generate for example a QGIS project file that is associated with your exported data.
Regards
SAV