It's only set to be controlled by the mouse movement on the y-axis rather than via the scroll wheel, mouse movement is locked to the QAM while open AFAIK.
Although having it use the scroll wheel would be nice.
It should be displayed in the first option menu provided (yellow one) as the second option is Partner interaction and the third is speech.
You have to aim at the vehicle in the checkpoint using the ALT key (remember that little red/white square that pops up?)
So, to clarify: Hold ALT and aim the white square at the vehicle in the checkpoint (it should go red when over the car), Open the QAM with CapsLock (while still ALT aiming at the car) and then use the mouse to select the option to wave the vehicle through.
Some of the QAM options are conditional, in other words they only display if you're doing something to cause them to display, like aiming at a ped or a vehicle with ALT.
It wouldn't make any difference if they made them or if the API plugins did. All callouts done by the API plugins like Callouts+, WoutersCallouts and TheWasteland get managed by the LCPDFR engine in the exact same way that the internal callouts are managed.
The crashing issues are not because it's an API callout but because of a bug or problem with the callout's code itself (this could happen with LCPDFR callouts in the same way). This is something you should report to the respective developers because we can't fix it if we don't know it's broken.
The dev's made an API for a reason, so people like myself could make new callouts and features that integrate with LCPDFR itself.
Only the partners should be using the flashlight as it was an experimental feature as far as I am aware, so to turn it off simply...don't use a partner. I know that sucks but at least it's a temporary solution.