No it's a production manufacturing thing.

The other ends of the tubes have to meet other parts, ie. head tube or frame ends, so the BB shell is where they take up errors. Given the choice to err short or long, most better builders prefer to go long rather than have a weak joint.

Back when we imported Italian frames, they used to run a specially made hole saw through the BB to clean up the tubes before tapping. On those frames, we'd see thread marks on the ends of the chainstays, proving they originally extended into the shell.

--------

Re, the hole saw. 1-5/16" hole saws are rare and may be pricey. OTOH- a 1-1/4 saw wont work without some help. If you just try to run it through the cutting forces will cam it over to the unsupported side, and you'll strike out. To make it do your job, make a pad covering the lower 1/3rd of the BB shell, to support the cutter and hold it just shy of rubbing the high side. This way it'll cut the tube more flush and not cam over.