5V is bad for T_4.1 that should not see more than 3.3V on any pin - except VIN or VUSB.
As far as interrupts - that would only be a few thousand per second with multiple encoders triggering. The T_4.x can handle a million well up to a couple of million before it gets swamped. If it would work well for encoder processing ... that would be an interesting test.
... Seems another thread with multiple encoders posted recently ???