Hi. The warnings could be caused by various things. As you provided very little information of the tools you are using, I can’t really guess. This sample project was done some few years ago, a lot has change since then: new FatFs versions, New MCC versions, new MPLAB X IDE versions, new XC8 versions especially the new v2.
And warnings are not necessarily gonna make your project not to work.
Are you testing already with hardware?
The SPI low level functions are handled by MCC. Check the SPI.C and SPI.h files generated by MCC. They’ve got nothing to do with FatFs.
It all gonna depends on what you are trying to achieve, the PIC you are using, the amount of resources required and the required features.
FatFs is quite popular, you might get support from many forums and it regularly maintained. It’s main advantage, it can be used by a variety of microcontrollers, not only the PIC.
Microchip MLA could be simple to use as it will fit easily together with other microchip tools like MCC but at the moment it does not support 8 bit microocntrollers like PIC16F and PIC18F series only 16 bit microcontrollers.
You an try both and see the one that will work for you.