It's certainly been my experience that getting a new, completely handmade, and complex "expedition" boat "finished" takes a year, give or take. How much is "commissioning", vs warranty work, vs just getting the boat set up and outfitted the way you want it are somewhat arbitrary lines. Perhaps more meaningful is what the builder is responsible for and what the owner is responsible for. But it all has to get done.
But one thing that's been interesting to me is that in my moments of frustration when I complain to one or more people who work in the marine industry, they uniformly say it's typical, and that Nordhavn is actually one of, if not the best of the builders. That doesn't mean there isn't room for improvement. There certainly is. But it's also good to keep it all in perspective.
It would be interesting to hear from others who have built new boats in say the 60-75' range, how long it took them to get the boat dialed in. The test for me is the marine supply/hardware store run. When you come into a new port, how quickly go you run to the marine supply or hardware store. When that stops being the first thing you do at every port, the boat is ready.
Smaller boats I think are different because they tend to be built in larger numbers and with less variation from boat to boat. Plus the systems are fewer and less complex. And when you get into much bigger boats, I expect there is much more professional project and production management. But I have heard plenty of horror stories in that range too.
We have built 4 boats, if you count the one just sea trialed and which we'll have a shakedown cruise in May. One has been in the range you say, three larger. However, they've all involved less customization than yours. We've also purchased one new boat in the 60-75' range. They've all been fully ready when we made final acceptance of delivery with all equipment installed and no issues from survey or punch list.
I would say two builds were from a builder who always delivers turnkey boats on time and on budget. It's the way they do business. However, they are a semi-custom, not fully custom builder. Equipment doesn't vary, just interiors.
One other was semi custom, more production than custom, but based on what others have experienced from them, we were lucky. They use a dealer network that we bypassed. They had a dealer in South Florida that was a nightmare and one for Miami and Central America that has been very slow in warranty. Now another in Fort Lauderdale that I think will be good based on the yard they now own. Then the one just built in Italy has frankly surprised us as it had the most customization, although still most equipment basic.
As to Nordhavn being one of the best. I'd say their commissioning process and equipment to be installed by the owner is very much on the high side. They deliver boats with much to be completed. I would put their number of warranty items and the length of time to complete them in the middle. They are known for taking time but eventually doing it all. There are half who do warranty quicker but then half who never do it all and you end up getting it done outside of warranty if you want it done. There are manufacturers who I would never trust on anything and they never get boats right. There are others who build a decent boat but are horrific on warranty due to the dealer network they use. As to Nordhavn's more direct competition, those like Selene, KK, Cheoy Lee, Outer Reef, Horizon, Hampton, Offshore, the competitors listed generally complete the work in less time. Now part is that the others don't typically engage in the ongoing modifications and changes during the build of the boat so some of the Nordhavn issues are self inflicted by buyers in cooperation with the builder. Nordhavn is known for not saying "no" and that is to a fault.
On the other hand I can name many builders I would tell people to never consider and I wouldn't say that about Nordhavn. I'd just say with them to know what you're getting into. Yours is a somewhat typical experience, other than the cargo issue in that it's taking a long time and many of the issues are entirely unacceptable (like the Lewmar where hatches are piled up and yet they continue to use them and they should never reach the customer leaking anyway) but then you do have confidence they will ultimately fix everything. There are builders such as Marlow and Azimut who build in this range and Marlow typically won't ever get it fixed while Azimut will in Europe but not in the US.
You mention what the builder is responsible and what the owner is. Nordhavn leaves far more than most builders in their size range for the owners to be responsible for. Their owners seem to like this though and you're right that it lengthens time and confuses the issue. They install far fewer items at the factory than most. Their buyers love selecting every item themselves and arranging installation. The ability of the buyers to select equipment and vendors, even of what the factory installs, adds to the problems. It's a lot easier to be trouble free and to provide quick warranty service if you only use one brand or, at most, two. For instance, no one has an issue with Nordhavn's hull or structure as they are pretty much standard and production. Standardization greatly reduces risks and issues and Nordhavn does less of it than even many major yacht builders.
The way Nordhavn operates is not inherently good or bad, it's what they do and their buyers are use to. It's just one way of doing things.
If grading them as a builder, I'd give them a very high grade. They build a solid boat. They're honest and fulfill warrantees. If grading their methods and process I'd give them an A+ for flexibility and a D- for delivery and those go together. They don't deliver a finished boat and they take too long to do warranty work. Again, the Lewmar hatches are an example of horrific performance on their part. They're sometimes sloppy as in the cargo.
I'd love to hear from those who have had Selene, Outer Reef, larger KK's, Horizon, Hampton, and Cheoy Lee built and their comparative experiences. Perhaps yours and my post should be taken to a new thread for that. If you so request, I'm sure the mods will do so. Label it "Comparative New Build Experiences" perhaps.