Interrupts can occur in either native 65C816 mode or in 6502 emulation mode. There are separate interrupt vectors for each mode. Looking at the CX16 KERNAL source code, the native mode interrupt handlers just switch to emulation mode and then jump to the emulation mode interrupt handlers.
This is also mentioned in Appendix F of the documentation:
The Commander X16 operates mostly in emulation mode, so native mode interrupts on the X16 will switch to emulation mode, then simply call the 8-bit interrupt handlers.