I'm familiar with the issue. What happens is generic controllers for hobbyists will have 12-15 cheap connectors (and only need six of them) , while a controller used on a manufactured ebike has two to four molded cables.
I believe that probably most molded motor cables follow the pinout used in Bafang motors. In any case, I have seen two bafangs and several non-bafang hub motors, and the motors all could be plugged into the same controller. However, the handlebar harness is probably different between different makes. I bought the Luna 25A controller that was intended to replace the Sondors fatbike controller, except I didn't have a Sondors. Only the motor cable fit. It was a lot of electrical detective work to splice in the brakes, display, and throttle to the handlebar harness. It was quite a powerful controller though when I finished.
How much extra money is it? Probably worth paying $100-150 more, unless you've got good analytic skills and good soldering skills. Plus the finished cabling will look better and be more reliable. Plus you could upgrade to the torque sensor later, which is probably a good thing if you stay with the Juiced boxes.
If it's $500 more, well you could buy a new controller plus all the controls and a motor for that kind of money, except you still might get those 12 jinky connectors.
As far as tweaking, probably a lot of marketing BS in my opinion. He's probably just adjusting some registers that are predefined in the user manual. If he is actually rewriting the controller firmware, well no one does that, aside from some experts over at endless-sphere who have reverse engineered the firmware for some common KT-controllers, and are taking on the Tongsheng TSDZ2 mid drive.