There are many differences between the T3.x and the T4.x but nearly all of them are handled by the Teensy drivers.
The T4.x are NOT 5V compatible like the T3.x is the main thing to be aware of.
Putting greater than 3.3V on a T4.x pin WILL kill...
I wrote this article for the unofficial Teensy wiki some 2-3 years ago that outlined the major compatibilities between the Arm based Teensies that use through hole pins (i.e. not the Teensy 2.x boards, and not the Micromod board that Sparkfun...