Finally managed to figure out how to allow manual activation of the afterburner within a certain throttle range, but still prevent it from being automatically activated. :)
The afterburner function in FSX was designed to be activated at a certain throttle setting, which is not how it works in Draken. You should be able to set full throttle without afterburner, then activate it with a key command. To cut off the afterburner you throttle back below ca. 95%. You should be able to regulate wet thrust slightly by moving the throttle within the 95–100 percent range on afterburner.
The afterburner_throttle_threshold value in Aircraft.cfg determines the throttle setting where afterburner is toggled in FSX. If you toggle the afterburner with a key command, the throttle will also be set to this value. Now, setting the threshold value to zero prevents throttle-induced activation, but it also means that the throttle will be cut when afterburner is deactivated. Setting the threshold value to >100% instead will apply full throttle whenever afterburner is toggled. Neither is what we want.
The solution was to set the threshold to zero, then add a gauge function which stores the throttle setting every update cycle, and returns the throttle to that value if the afterburner is toggled. It also adds its own cut-off function so you can regulate wet thrust within a set range. Voila!