I posted this in another thread, but still relevant.
Most builder's websites will say "Here at XYZ Builders, we build custom homes..." However, my thoughts on what a custom home is versus some of these builders' thoughts on a custom home is are different.
Let me give you an example. Say I own a franchise and we'll call this franchise...McDonald's. We specialize in hamburgers. In fact, we will custom make your hamburger. No pickles? No problem! We will custom make your burger with no pickles. Want ketchup instead of mustard? We will customize that for you as well. In fact, we do custom so much, we consider ourselves a custom burger maker.
To everyone else in the world, we call this "build to order." The moral of the story is, some of these builders let you pick out your countertops, style of cabinets, paint color, and fixtures and call it a "custom home." So when you're picking a builder, I would stick with the ones that more than half of their work is custom floor plan homes. That doesn't include moving a wall in one of their plans, but true custom floor plan homes. That would be the first weed-out question I have before we went any further.
We did not ask that question, but we did look for builders that specifically said "custom homes." That caused us several delays. Most of the builders will say they can do it. They probably can. But I would still advise going with someone where that's the majority of their work. If you see a builder that says "Design-build," that's probably where you want to start.
Hope this helps! While we don't have any specific experience with either of these builders, from talking to them, Kolby Homes, Magruder Homes, and Schaefer Custom Homes might be worth looking into. We're still finalizing finding a builder ourselves.