This is unless of course that ATC cards come with their own PCI express card with these functions.

I am going to assume that high end CNC control boards probably have ports for ATC functions as standard.
All you need is a breakout board that has 24V inputs and outputs. There are no special ATC functions, just inputs and outputs. You can use the same input for a pushbutton or limit switch as you'd use for an ATC sensor.