I pull my wire in the receiver box to the point where there is still 40cm of antenna wire on the outside or an extra 2 inches past the tube. Works fine. Once again all my friends calls are setup the same way lol. We do all have failsafes though, but they never kick in when the vehicles are far away. So you don't cut it just put some of the wire on the inside of the receiver box. Try to keep the wires tidy from the wires on servo and the battery. I usually shove it behind my recever box or on the same side coming out with the antenna of the receiver. Hopefully you have a failsafe just incase it does create a signal issue. If you run spektrum 2.4ghz radio systems you barely need any wire coming out of the receiver box, actally you don't even need a hole in your body to be honest you can jsut run it from the inside with spektrum because it's so short.
You can kind of tell in this pic how i shoved the wires on the same side the antenna wire comes out of the receiver. I have to take a clear pic later or tomorrow with my actual camera.