I suspected that but it also seemed weird that it was only me who had this problem so I felt pretty sure that I had configured something wrong.
I haven't looked too much into MTP libraries for finding the full path of the SD card, for now I have looked up the path manually and set it in my python script. I'll have a look at wifi sync but I guess I'll have to stick to running my script for now.
I'm a bit curious though since it seems like not many people have encountered this problem, how do people usually configure devices and playlists when using an SD card?
Or do people just buy phones with large internal storage?