That build was a non-PBG kit. I sourced all the parts individually. Whilst it wasn't a scratch build, I did a fair bit of custom work to the body, neck and components.Did you use the factory electronics (and add the mini toggle) or did you upgrade pots and switch as well?
I have not done a PBG ST type kit, but I believe (someone please correct em if I'm wrong) that upgrading to full-size pots is not an issue as far the routing is concerned (unlike the TL's). Not sure about the depth for a proper CRL or Oak Grigsby lever switch though.
That said, and TBH, there is really nothing wrong with using the stock pots or switch.
I think sometimes we (myself included) can get a bit too "cork sniffy" about some of this stuff. Yes there are higher quality components, but CTS pots aren't going make me a better player or make a HUGE difference in "my" tone.
As a friend of mine says "Tone just happens".