In some cases such as in Stratocasters with 3 pickups, having the pickups too close will cause unwanted harmonic overtones on the lower strings especially when playing way up the neck. The strings become magnetized from the 3 pickups and the notes become very indistinguishable. At times repairman and builders use height adjust springs made of spring steel and surgical rubber. At times the surgical rubber is cut too long and needs to be trimmed to get the pickups up a little higher. Pickup and bridge height have lots to do with the angle of the neck. This would need to be looked at by a qualified repairman to see if any thing can be done to change the neck angle for better pickup height.