I think each builder is a little bit different. And I think your observation is correct about time vs degree of customization. Some builders deliver a very turn-key boat, more so with smaller boats, but not always. Others leave more to the buyer's choice, or are happy to let the buyer choose if they want. Nordhavn will deliver a very complete boat if that's what you want. The N68 after ours arrived later and was done and gone in 6 weeks.
And this reinforces the need to fully discuss all aspects up front. Know your builder. Know yourself. Be honest and thorough with your builder. We were building about the same time Twistedtree was. We had someone on site for the entire year of the build. However, when we went for the delivery, the boat was complete, everything done, ready to cruise. We did a 2 week, turned into 3 week, shakedown cruise with a factory employee on board and did any adjustments during it, then returned it for checking everything and oil change and such. Twisted customized nearly everything imaginable. We customized the living area but we chose all equipment up front and the vast majority is what they always put in this model.
Two completely opposite ways to do it and we're both very happy with the process and the results.
Taking that a step further, I'd not enjoy the TwistedTree approach and I'd be willing to bet he wouldn't like the less creative approach we took. But then why would that be surprising when we chose boats as opposite as possible.
Major warning. Do not coerce a builder to try to get them to be something they are not. We had a guy here and elsewhere who sued Nordhavn over the 120. He basically sued because they didn't do it like Westport, all on a precise schedule, all the same finish. They were desperate and agreed to do so but clearly never paid attention to those contract clauses. Oh, and Nordhavn won the suit completely. Similarly, don't go to Westport and try to change everything. They'd wish you well on your way out.
A very good builder of larger boats was Burger. They agreed to do a bunch of things they'd never done on a gorgeous boat names "Sea Owl." The boat was to be built as the most secure ever with all bullet proof windows and electronics and many other things. It was a year or more late due to the builder and due to customer supplied items not being ready. All in all a big mistake. The owner actually started a contract on a new build before it was ever complete and this "Sea Owl" was build by Feadship. They have the experience and versatility.
Don't expect a Ranger to be built like a Hatteras. Add that much weight though and you'd really be disappointed in one.
There are many ways to do it, but find a way that works for you and the builder and where you both can do your part. One thing, even with the builder who delivers turn key, is a lot of choices and decisions along the way and if you aren't prepared to make all on time, don't do it. On a semi-custom to be delivered ready to cruise, there are literally hundreds of items. Many decisions remain, just are made at different stages of the process. We chose watermakers and generators just like Twistedtree, just did so in time for builder to install them. We didn't get a choice on engines or thrusters or stabilizers or interceptors.