It would be nice to have a definitive account of the nature of the deal between Fender and Kubicki. I know that it was a licensing deal, but the manner of the production seems to be a matter of some discrepancy. One thing that is obvious just from the serial numbers is that the rate of production during the Fender years was much, much higher. In two years or so, many more basses were made than during all the other years combined. If Phil was indeed making them, he must at least have had some help, or automated the process in ways.
I have had all four production models, so to speak--a pre-Fender, an early Fender (18v), a later Fender (9v), and a post-Fender. The differences between them were pretty subtle. If I had to rank them, I would put the post-Fender as the nicest (exceptionally resonant body), then the early Fender (I still have this one, a fretless 34" scale Factor 4--best fretless I've ever played), the pre-Fender, and then the late Fender. I put that one last, but it was still a really great bass. It was just a tick away from the others in terms of fit and finish (although still way better than ANY Fender instrument I've ever owned) and I prefer the 18v. preamp for more versatility. I think like anything else, there will be variations between instruments and they would really need to be evaluated individually.
From my experience, I would have been tempted to buy that yellow one from The Low End had I spotted it. I think the Fender licensed Kubickis are among the best deals in used basses. If one is in good shape, and especially if it has the 18v. electronics, there would be very few basses in its class available at any price.