Using TFT with hardware SPI and speaker with tone()
You are getting your wires crossed in your brain and imagining a problem where there is none.

Both PWM on pins 3 &amp; 11, and tone(), use the Timer2 device. Only one of those can use Timer2 at a time, and they both want to use it in different ways, so there is a conflict between them.

Timer2 has nothing to do with SPI. So tone() has no effect on SPI, and nor does PWM have any effect on SPI (other than the fact that only one can come out of pin 11 at any time), since there is no internal resource conflict.