The Vision+ is a strange system and is not for use as a serious data collection platform. It records the geotags (badly) and doesn't record any altitude data. It is possible to use the EXIF workflow, but the results will be poor due to the lack of precision on the geotags directly from the Vision+. Pix4D limits the altitude you can fly to 50m and then takes that knowledge and uses it in their processing. It is a good workaround, but isn't very flexible.
For accurate mapping using the Vision+, one should use our Basemap or Manual workflows. These take the geotag imprecision out of the equation and make the map as accurate as you can place the GCPs or manually record and select GCP locations.
All of our outputs are in WGS84 and can easily be converted to various other coordinate systems using 3rd party software.
The OBJ files contain all of the point cloud information in a readable format and can also easily be converted into other formats.