using sd card without using FAT

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Yes,

You can access the SD Card via SPI without using any file system.
 

Yes, its like a flash memory, but you need to read and write them sector-wise , that is when the sector size is 512 bytes then you need to read and write always blocks of 512 bytes.
 

Using a file system will allow you to insert that card in any windows/linux/android/mac machine and to read/write files, directories aso. Writing raw data, without a file system will make that card usable only for an application which reads raw data from the card and that application must know what and where it is written.
I had few years ago a device which stored all data from a CAN bus onto a sd card in raw format. Then I placed the card in a PC and with an application which works directly with the card (such as hex workshop) I was able to read data from it. But the PC won't see such a card as a valid drive.
 

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