Ask any guitar builder and he will probably tell you it’s because of the different materials used in each instrument. I have found that the lighter wood makes for a smoother sound and the heavier woods tend to make the pickups sound harder and brighter.

My favorite woods for instruments are Swamp Ash for Telecasters, and Alder (light) for Stratocasters. I can hear the difference between pickups from body to body. You must make sure you are using the same value volume and tone pots. Also the type of bridge used, neck material, frets, strings, finish on the body and neck, and how the pickups are adjusted. Also check the weight of the completed instrument.

Because there are so many variables, it may be hard for you to correct this, but a good builder or repairman can gibe you valuable information.