Starting on version 4.2 a new option will be available, the new option allows for 4 different filesystems, fat32 (default), ext4, exfat and ntfs to be chosen before the first boot. And its defined in one file in the root of the SD right after you flash it from etcher, the file should be called ee_fstype (NO EXTENSION!) and if the file does not exists then it will use fat32 as default, but if is exists and it has exfat, ntfs, or ext4 the partition will be formatted to that filesystem.
So instructions:
1.- Flash the correct image for your device.
2.- Right after it is flashed don’t take it out yet, open the first partition EMUELEC
3.- Create an empty file named ee_fstype (no extension!)
4.- Open the file and type your choice exfat, ntfs or ext4 save it and close it.
5.- Do whatever else needs to be done on the partition (dtb changes, ee_default.txt, etc)
6.- Insert on your device and if everything is OK you should see the first boot formatting your desired partition.
Please note: This is an experimental option, it is still being tested and it is not yet final. But this will hopefully help those people out that do not like fat32 as their FS choice.