I should probably make something clear;

It is very good troubleshooting to take into account what was done with the car in order to guess at where the issue is. You did good in this respect - but you cannot take that assumption too far. Proving the validity of the latch switch's indications to the PTCM is easy and should be step 1, based on your suspicions.

TO do so, do this:

1) Tear the trim from the trunk around the PTCM.
2) Jam your positive meter lead into slot 17 of connector C1.
3) Ground the black/negative/common meter lead by clipping it to a ground bolt or by jamming it into the slot 11 of connector C1.
3A) You will need long enough meter leads to put the meter outside the car when you close the lid.
4) Close trunk lid, start engine.
5) Manually fold the top up away from the lid and use the top tool to manually latch and re-latch the tonneau lid using the tool to rotate the cam.
When doing this, the meter will jump from zero to about 5 volts (I cannot remember for sure, but I believe the voltage is 5 when the lid is up and zero when it's latched).

If this rolling from 0 to 5 volts occurs, the tonneau latch switch is fine. THis does not prove the hall effect sensors on the latch cylinder are OK.