There's always a depends. I went with a custom builder. I didn't build. I remodeled and added a 2500 sq ft addition onto my house and bricked/stoned the house. What I was saying is that all the custom builders I interviewed would certainly install anything you gave them, but if you bought a shitty $1k tub from lowes because you didn't want to buy the more expensive Kohler tub, the plumber might not warranty the cheaper tub. Plumbing was really the only place I ran into this. Everything else was our choice. Our basement is a heated slab, and I've been happy we went with the boiler. We've tried our best to run it out of hot water and haven't been able to. Most builders are not going to be ok with the buyer showing up with all the lumber, brick, plumbing, electrical, etc sitting in the driveway and telling the builder to build them a house. I pushed the limit of any builder's patience with my attention to detail and overall expectations.
We were given some hard numbers and thankfully we were within 10% of the original estimate. At least 5% of that was stuff I just decided to add midway through (barrel vaulted bedroom ceiling with l.e.d. Starlit sky), etc. in the end, I wanted to have the best house in my neighborhood. We loved the lot, and basically spent what we originally paid for the house to add onto it and remodel.