It has been awhile but @brtaylor's links but you would need to for sure do things like core_pins.h and pins_teensy.c
And probably be able to add the extra pin numbers.
But depending on what it is you are wanting to do that may only be the start.
For example if some of these pins do Analog and you wish to use them as such. You may want to add them to the analog code..
analog.c ... Unless of course you wish to use ADC library than may need to change it as well.
Then there is Uarts, SPI, Wire, ... Some of these you can change directly in the core files. Like our SPI library has tables which you can add the extra pins for which are valid for MISO, MOSI, SCK, CS... to the tables within SPI. But that may not fix all sketches and libraries, as many still do their own code that checks is the MOSI pin x or y...
But it is all doable. All sort of along the work that it is taking to distinguish between T4 and T4.1