From what I can make of the submission, this technology is really only beneficial for NH-22C Yamataians.
Because the SPINE interface gives the neko the ability to completely immerse themselves into the vehicle and use it like it was their body.
SPINE is nothing more than a physical interface which allows one to connect to a software system. It's the software system which allows the Neko to communicate with the target device.
The Integrated Electronics System, what the SPINE connects to, it what really allows a Neko to immerse themselves into a vehicle. This submission is a suite for operating within the Integrated Electronics System which enhances that ability -- especially for future vehicles designed for it. It can be run via SPINE and helmet/headrest sensors for Nekos or through helmet/headrest sensors for a Yamataian.
In summary, It enhances a Neko's SPINE experience and better defines it for craft designed with this software in mind, and also gives Yamataians the ability to utilize it.
Also how does the system avoid stray thoughts interfering with the controls.
People tend to think all sorts of stray thoughts when performing tasks. In the heat of combat, even more so.
As for stray thoughts, the actual movement commands are sampled from the motor control section of the brain, allowing both reflexive action as well as actual decisions to move. Stray thoughts aren't as much a concern there, nor in the sensory areas of the brain which the sensor data for the vehicle is fed into. The decision to fire or select a fixed speed is done more by command and will, and can be affected as you say, but no more so than a pilot in an existing Power Armor who happens to get distracted or fires on impulse.
The sampling of thoughts being made difficult by your concern is more for the tactical part of the suite, and it actually does have to cope with these problems -- it takes time and practice for that program to adapt to a pilot's line of thinking, and if the pilot is unfocused, it will show in the system being unable to as accurately predict the next move of the pilot as and prepare the relevant systems(joints, thrusters, etc) for it.
Because of all this, the tactical system will simply perform better overall with a focused pilot, but an unfocused pilot will still be able to control his craft without problems. No system is perfect; and that particular shortcoming can be overcome with practice, skill, and focus -- something which can actually prove beneficial for RP.
And if its using some sort of telepathic form of communications, how is it protected from people sending telepathic thoughts to the operator.
This merely deals with new software within the existing Integrated Electronics System and its existing telepathy protocols, so existing PSC technology can still serve this purpose in the exact same way it has for years.