The reason is, at least with Samsung devices and cards larger than 32GB, Samsung or Android formats the card with the exFAT file system, but incorrectly identifies the partition type as "FAT32 (LBA)", or partition type "c" or "0c" in the card's partition table.
If you format the card with exFAT using Windows or the Android partitioning app Aparted, it will correctly declare the partition type as 7 or "07" for "exFAT" (HPFS/NTFS/exFAT) in the microSD partition table.
I have struggled with this same problem, and just confirmed the above information by formating a completely blank, unpartitioned 200GB microSD card on a Samsung Galaxy Note 3 with Android 4.4.2, and in Windows, and using Aparted on Android.
If you are trying to recover data from a card that was formatted with exFAT, but whose partition is incorrectly identified as "FAT32 (LBA)" or "c" or "0c" in the partition table, I believe you will need to force the recovery app (e.g. Testdisk) to identify it as HPFS/NTFS/exFAT or "07".