MP uploads what the autopilot requests using the best available data it has. in your case this will be the geotiff.
the name of the folder was simply because that's what already existed. it does not mean anything.
the terrain system was designed around the srtm system. if the folder on the sd card is called this, it agains doesn't mean anything, as the data it contains will be the data MP uploaded, which could be from the geotiff.
id be pretty confident that you already have your geotiff data on your pixhawk. its just the folder naming was designed and based around srtm. not geotiff.