Doing so would compromise the performance of your transponder. The quarter wave stub vertical antenna you are using should be mounted perpendicular to the ground plane. A sufficient ground plane is required for this antenna to operate properly. The size of the ground plane required for optimal performance of a !/4 wave monopole antenna is determined by the frequency you are transmitting, in this case, around 2.5" radius is required. Mounting it at 45 degrees, or any angle other than perpendicular for that matter, will affect the impedance of the antenna, thus increasing the reflected power (SWR). This may result in damage to the output amplifier in the transponder. I suspect that some of the newer solid state transponders may have built in protection for this.
Could you possibly mount it under the pilot or passenger seat?
RV-10 - 890
First Flight Oct 2012
Aviation Partners, LLC