If the signals can be both GPIO and something else, then they are normally 5V tolerant in both modes since the special peripherial functions are normally using identical logical input/output levels.

But there are of course exceptions.

The most common exception is probably that the ADC input MUX may be 5V tolerant, but not the ADC itself so when the pin is mapped as an ADC input, it will no longer be 5V tolerant.

Then there are I/O pins that are different because they are intended for specific use and can't be implemented identical to other signals. I2C for example uses open-collector/open-drain. And the USB pins have to fulfill the requirements of the USB standard. But these signals are normally electrically different in any configurable mode.