Maybe. It depends on whether the trunk location provides enough distance between the tower antenna (outside antenna) and the device antenna (inside antenna).
If the two antennas are too close together, they pick up each other's signals and create a feedback loop condition called oscillation.
By FCC regulation all cell phone signal boosters must auto-detect oscillation and when this condition is detected, immediately reduce power or shut down to end the oscillation.
An oscillation condition is corrected by increasing the separation distance between the antennas. When the antennas are sufficiently far apart, the signal booster can operate at full power.
When a magnet-mount antenna is located on a vehicle roof as recommended, the metal roof acts as a shield - blocking each antenna from picking up the other's signals. But when the antenna is located on the truck deck, there is no shield to prevent oscillation.
In this situation antenna signals may pass through the rear window glass creating oscillation, unless the separation distance is sufficient.
You'll probably need to test the trunk deck antenna location to observe whether your signal booster can operate at full power. If it cannot, then the roof location is your best choice the magnetic antenna.
As a general rule, cradle boosters like the Drive 4G-S and Drive 3G-S typically work fine with the magnet mount antenna located on the truck lid. For other booster models, you will need to test the antenna trunk location as described above.