Hi Francois (or whatever your real name is), how are you?
Nice idea but using that method (apart from the reliability of the results using a bluetooth speaker) only measures the frequency response and eventual non-linearities of the pickup itself but tells you nothing about its magnetic aperture (i.e. the portion of string it "picks up"), the effect the instrument scale has on it and its position (neck vs bridge, etc.), these things might not matter that much in your example but would definitely matter when trying to copy the sound of a pickup in a different position or on a different guitar.
In that case, in theory, it'd probably be better to simultaneously record (somehow) the two pickups with normal playing and use the dry-wet pair method on tone3000 (I've done this myself with an acoustic piezo output and mic with great results), or maybe you could even get good results by using something like Sonulab's MagicMatch if you can't record them simultaneously.
But in practice, using different positions also means different null points in the frequency response of each string, which can't be fully compensated by nam (you can't infinitely boost a frequency) and results probably wouldn't be very accurate anyway... that's why for this kind of things it's usually best to use piezo saddles or hex pickups placed very near the bridge, cuz at the node (aka the point where the string touches the saddle) there are no nulls and your signal will be a blank canva frequency-response-wise.
EDIT: check these links for a deeper explanation of what I'm talking about and for a simulator
https://till.com/articles/PickupResponse/
https://till.com/articles/PickupResponseDemo/
PS: I think this idea could greatly improve systems like Variax, Antares ATG and Roland hex processors, cuz the major drawbacks of those have always been the pickup response simulation... Using a NAM model for pickups instead of a simple IR/filter might produce great results.