Susquatch, I like the way you think. I am also an engineer by training, Aerospace to be exact, though I haven't used my training in many years. I got into rifle building, or as others have termed it probably more accurately, "gun plumbing," because I wasn't content buying a precision rifle. I wanted to understand why a precision rifle would cost $2,000-$3,000 more than an off-the-shelf rifle. So, I took machining classes, watched all of Greg Tannel's videos, bought lathes, and mills, and fixtures, and tools, and reamers, and gauges, and, and, and... I am convinced I've built some of the most expensive rifles in the world, and so is my wife!
Not the best in the world, just the most expensive.
Anyway. Of all those rifles, the one I have kept over the years is the one I put the most effort into. On that particular rifle, I started with a stock Remington 700 short action receiver. I used a piloted raceway reamer to cut the raceway to a consistent diameter. I then recut the threads using the reamer, which was perfectly aligned with the raceway, as my datum for indication. Then I refaced the bolt lugs and receiver face. I then purchased a new single piece bolt from PTG to match the new raceway diameter and hand-fit it so there was just enough room to slide smoothly through the receiver, but not enough to allow unnecessary slop either. That bolt, despite being a precision made component, was also hand-lapped to mate perfectly to the receiver. I also machined a cut out to install a side bolt catch. Then, I purchased a brand new Bartlein barrel blank and indicted it in on the lathe using the bore as closely as humanly possible and proceeded to cut the tenon and chamber it slowly but surely. I put it all back together with a Timney trigger in a Manners stock and wouldn't you know it operated like butter and shot like expected.
So, all that to say, I now know why custom rifles cost as much as they do. If they're done right, the smith is putting a lot of time in the details. All the time and attention results in a rifle that will operate consistently shot after shot, and that's really were the precision comes from. Like you said, as long as the rifle and shooter do the exact same thing every time, the result should be consistent...as long as wind, and air, and etc. all do "their part."
I don't build rifles to make money, or to save money. I do it because I really enjoy seeing the results of a lot of careful effort. For me, that's the joy of it.