Hi there,
I do!
So on the ESP32S3 the SPI is different, than the C3 for example.
Have a Look the Demo code on The Xiao Grove Expansion Board with add-on Flash chip.
The chip supports differently the SPI busses, Also QSPI or Some modes are reserved for on board.
As long as you define the custom pins in the sketch NO NEED to modify the pins file. 
(they all support pin multiplexing) That should NEVER be except last resort.
Are you trying to use a Flash device or an ordinary SPI device?
can you post the code using the Code Quotes… We can see what is the issue.
HTH
GL 
PJ
What is the hardware connections you have?