The LT40 is very forgiving for a wide range of power choices. The 40FP will be excellent for the use on it. Sure, not the higher power output of the 46FX, but it doesn't need it at all, either. General performance will be about the same, although you may not have the same strong vertical abilities or top end speed. But its a trainer, and doesn't need those. Good plan to reserve the FX for later use on a plane that can better use it - the Ultra Stick.
Play a bit with prop sizes - you may be very surprised at how the LT40 performs using a 12x4. Top speed will be lower, but it will pull through almost anything extremely well - and allow you to slow down for landing even better.