To me the Custom shop is about getting a bass you want, not just vintage reproductions.
I got a Fender Custom shop Custom classic Jazz bass second hand. Played beautifully, looks amazing, doesnt weigh too much. Was equipped with Fender N3 noiseless pickups and a fender 3 band pre amp. After 18-24 months of playing it I could not get a sound out of it I really liked. To me it sounded ok, but not amazing. I didnt sell it as it played so well. Fitted Nordstrand pickups and a custom East pre-amp and its became an incredible sounding bass (IMO) gigged and recorded it sounds exactly how I want it to.
D-tuner now fitted, luminlay side dots fitted and its now a bass I'll keep til I cant play bass anymore. Versatile, comfortable sounds and looks great, again in my opinion. Perfect jazz bass for me. It took a big leap to mod the bass though...but so glad I have done it now.
Jonny