90% of the time when I want to set a location im already moving with WASD, so when I click with the autodrive tool it does a drag interaction instead of a click, which briefly brings up the selection marquee rectangle instead of setting the target position. Would it be possible to (say) press right click which would force it to set the target location at the clicked position?

The problem is that the keys are a selection tool – and those select areas. As far as I know, there is no way to register a click. Instead, the mod interprets a selection of a very small area (with a very small distance between top left and right bottom) as a click. Thus, if you try to click on a position while you're inside a moving vehicle, it's close to impossible to finish the click before the selected area grows until it is interpreted as area selection.

However, last time I checked you can select a new destination from inside a moving vehicle when you switch to map view. Does that work for you?