Don,
Your suggestion to use SL antenna only for the design (disconnected) and to connect another antenna to the amplifier itself is ok (and maybe a very good and sympliest solution : no modification of the amplifier, can be reversed, ..).
However, you should find a suitable place for this another antenna.
Some important points :
a) antenna shall not touch metal part (very important)
b) antenna should be vertical as much as possible
c) every metal part around the antenna will act as a shield (i.e the antenna will not receive anything from this direction) : example : if you put the antenna in the trunk, if the trunk is open, antenna will receive. If the trunk is closed, no reception (or bad reception). Therefore, you will not be satisfied with your idea to put this antenna in the trunk.
d) antenna basis should be connected to car body
Point a) is mandatory.
Personnaly, i would go for this antenna in the bumper (see my picture), on the rear left angle, Upside down (it should be easier for the cable) :
- point a),b) will be ok.
- For the point c), at this location, the antenna will have some directivity (antenna will be able to receive signal from emitter located in the rear part of the car, and it will be more difficult for an emitter located in the front right side of the car (all the car will act in this case as a shield between emitter and antenna. However, in suburbs or city, impact may be neglictible)
- point d) will not be done
The result in this position shall be much more better than the SL antenna. You can try it easaly : connect your new antenna to the amplifier, and use adhesive tape on the external side of the bumper (with removing it). You should be convinced with a short run that it is ok.