pros of internal brake cable routing are mostly that people like it; I think yours is the first case where there is any practical advantage. Cons are it is more work, so I'm sure there will be a charge for it. Some builders really hate doing it. It has never really been my style, but I'm about to do my first internal routing. Typically, the cable goes in at the rider's 7 o'clock and comes out at about 11 o'clock. Here is a photo sequence from Richard Sachs,
link Many builders put a reinforcing plate at the ends
If you are having a framebuilder do this, he will want you to fill out a questionnaire that would spec internal routing. Most builders use bikecad, and that detail doesn't show up on the drawings, it's on a list of specs.
There are people that use internal routing for the derailleurs, but I would not do that myself due to the requirement to unnecessarily pierce the downtube. The top tube really isn't compromised by the internal routing. There have been corrosion problems when companies have taken shortcuts, but everyone uses a tube to fully sleeve the cable nowadays.
Disk brakes get close to tying you into straight fork blades and 135mm rear spacing. If that's ok, there is no real problem