Dodecagon being 12 sided matches the 12 Disciples.
12 being a Holy number.
Another reason is the light through the windows. Most Gothic era churches using a dodecagon type design at one end seem to be aligned to the vernal equinox. That would be around Easter. And the light would fall on the main alter at proper times.
This is just my thoughts. I figure others can chime in with thoughts and such.
