I understand OP's choices would not disagree with his choices at all
Here is a look at my decision on doing a custom with rim brakes
as a custom is likely a once in lifetime thing for me I looked at disc vs rim, electronic vs mechanical, pretty much all build choices
I choose rim brakes, after a lot of discussion with the builder. (It should be noted that builder was an early adopter of disc brakes and build a lot of disc frames)
Key points from the discussion were: what type of riding do I do (i.e lots of riding in hills with heavy loads) and what was a priority for me ride handling, etc)
the biggest point is that if I went disc brakes, the fork would have to be built heavier and ride and handling would not be as good a with lighter fork
I chose ride and handling and went with rims. other things that influenced the choice were a) I have really never had a problem with braking with good dual pivot brakes (check out the velo orange grand cru) and b) I don't see myself using carbon rims (aesthetic choice primarily)
My choice, not a right or wrong, but my thinking