If I am understanding your question correctly, you are asking if you have the Audio adapter setup on a Teensy 3.2, which uses several of the IO pins of the Teensy
to work, can you also use those IO pins for other GPIO functions....
My guess is do not put an SDCard in the slot and do not populate the memory chip location on the board, that you can get away with
using the SPI pins and the two CS pins, for other purposes.
With the obvious caveat, that if you use SPI for other things like a TFT display, than the MOSI, MISO, and SCK (alternate 14) will be used.
That is pins (6, 7, 10, 12, 14), but note: there is 10K Pull up resistors on the two chip select pins pins 6 and 10