Offizieller Kommentar
Yes. The images taken with Map Pilot can be used with any image processing software.
DJI aircraft do not record the altitudes above sea level. The altitude values in the geotags are relative to the take off point.
Maps Made Easy accounts for this by allowing users to upload a ground reference image with the rest of the aerial imagery. We use this image to pull an elevation value of the take off point from USGS or SRTM data.
You could do the same thing with your images by manually adding an offset into the tags of each of the images.
We don't know how Pix4D does things and can't supply specific support for their software.