I think you'll have to learn to live with the cable housing.
FWIW, ALL the internal-routed Miyatas I've seen are set up to run the cable and housing, even my high zoot Team Miyata Aero TT bike.
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You know it's going to be a good day when the stem and seatpost come right out.
(looking for a picture and not seeing it? Thank the Photobucket fiasco.PM me and I'll link it up.)