When you have a multi engine plane if you have an ESC on Throttle and throttle 2(There are 4 total) lets say Throttle is on Ch3 and Throttle 2 is CH7 the Throttle Cut menu item only programs throttle kill on the Throttle on Ch3, the 2nd engine remains active.
How do I get the throttle cut function to work on multi engines?

Throttle cut is meant more for IC engines. Regardless, in the case of multis I would use conditions with one of them having zero throttle on all the motor throttle channels

Here's a Model set-up for a HK BushMule twin where I have implemented throttle kill and differential throttle for the engines. Feel free to modify the model to fit your needs. I have used this model on a HK Albatross HU-16 also.

R/
Don