It would be possible to cut boards to the exact site in a factory. However, you would lose more in the logistics cost of managing all the different possible sizes that you need. Thus two by fours come size multiple of two feet except for the 92 and 5/8's and 104 and 5/8's. Those later too are the extremely common sizes that are used in most commonly.
The truck has to pass through something like Home Depot anyway because all those boards come not on a truck they come on a railroad car and then they'd have to be transferred to trucks to get them to wherever. That Home Depot-like place is also a good place to stage things if you actually are building you'll discover that the dedicated lumber yards are very good at breaking apart all the different pallets of lumber and they figure out exactly what you need and they put those all into one group and bring it to you. Yes, you do sometimes have to cut a 10 foot 2 by 4 and 9 foot 2 inches. However, you are never in the situation where you have a 12 foot 2 by 4, you have to cut to that size because Lumberyard has already figured that out and gotten you the closest to the right size for you. Having been in construction, I can inform you that there are very few boards that actually return to the lumber yard at the end of the build. They are generally right on and getting you the exact amount of lumber you need from the blueprint
I can really understand high ceiling (in new residential buildings) only for people who use fake built-in second floor (dunno the word in English, maybe mezzanine by my quick research) for like bed or something, but what's the point then and why not build proper separated 2nd floor if you are building new house
The big problem with kit homes ends up being what happens when (not if) you @#$@ something up.
And the big builders are already bypassing Home Depot, they buy from suppliers that you've never even heard of (the smaller ones buy from suppliers you've heard of, but when you went in everything was 5x the price of Home Depot, because they don't want you as a customer - they want the builders who buy on account and get 80-90% discounts on "list price").
There are some large-scale lumberyards that still have a railroad siding and will get lumber by the carload.
A delivery of lumber for a typical house is a full load (or more than one) via truck, and obviously a train isn't going to come to a construction jobsite. So the llumber at the construction site is already hand picked...
It's no big deal at all to cut off ends to make it fit exactly, but when framing most of the 2x4s, etc. are already the exact size you need. You just trim off the top and bottom plates at the edges of the rooms.