I'm on the landscaping & pool side of the business and work with several custom builders. There are about a half dozen builders I work with and each does it a little different. One does cost plus 20% on new builds (builds 10-15 per year). One charges a fixed management fee (builds 10-15 per year). One builds and sells it as a completely finished product (3-4 per year). Another is a custom builder that runs them like tract homes and does 350 a year.
If you have to have it 100% customized to exactly as you want it, go with an Architect. While they will claim they start from scratch, they'll take a floor plan the will work with your wishes and tweek it to fit. They will probably put in some expensive details to make it modern. But you will get a full set of plans on a (hopefully) well thought out design. If you are extremely particular, this is the way to go.
If you want to save $10-20K (or more) go with a drafting company. These are typically people who have worked for an Architect for a decade and go out on their own. They'll use a set floor plan and modify to fit. The kinks have usually been worked out by builders. You can many times see homes built off their plans.
You can make a house modern, rustic, modern-rustic, etc. by choosing finishes and colors. Even using the same floor plan, a house can look incredibly different depending on finishes. I do this all the time on my landscape and pool builds. I can literally do the same design and make it modern French rustic by using certain materials. I can make it modern by switching to other materials.
One builder I work with literally does that exact same floor plan over and over. They sell completed projects, and change them enough that they look different. White & black with limestone facing on one model to do the modern rustic farmhouse look. Painted brick on another with some metal siding to go modern on the next. The houses looks great and sell in the 2-3 mil range. That builder, when approached by people, say to use the drafting company that he works with and he will quote the project afterwards. Or they have to buy what he already has in the pipe line.
I would approach a few builders and get a feel for them. The builder will steer you towards the architect they work with or a drafting company. The builder is who will make or break the process for you. They can make it run smoothly or rough. They are who you will be working with for the 12-16 months and be who makes sure the quality is up to par or not. My favorite builder (E&S Builders) will not go out to Gold Canyon as they specialize in a 15 mile circle in N. Scottsdale/Paradise Valley area. The owner is honest and extremely hard working.
The other thing you have to decide on is the payment that you want to do. E&S does a cost plus 20%. You have to trust that he is doing thing right as cost can run over budget very quickly. They scare off the timid by quoting high ($500 per square foot) and actually deliver under budget. Because they are cost plus, it is dependent on the materials & options you pick. I had one person pay $5K in shipping fees as the interior designer suggested a concrete paver out of California. I'm working on one right now where the client wants a decking material from Italy. The US made material is better and the same cost, but he likes that it is made in Italy as it sound fancy.
Another builder I work with charges a fixed management fee. You pay them to manage and you pay the invoice from the trade that does the work. They do some pretty nice stuff as well.