Dan, you are obviously right that it is easier to distinguish small
interval-differences in harmony than in monophonic lines, where you must
somehow remember the previous pitch and compare that memory with the
newly perceived pitch. However, in your discussion of brain areas etc.
you leave out one of the most important methods a trained musician has
of remembering a pitch: muscle memory of what it takes to reproduce that
pitch. I believe that when you hear a recording of a RO your lips,
mouth, head, and fingers consciously or unconsciously move toward a
"rehearsal" of that sound, and when a subsequent TSU NO MERI comes along
those same muscles subtly adjust to the new pitch. The feeling of the
muscular adjustment -- which is often an extremely understated gesture
(invisible to the world) that is proportional to what the actual
performance adjustment would be -- is as much a part of pitch memory and
pitch discrimination capability as the more abstract and constructive
neurological processes you suggest. I find that sometimes I use
instrument-playing body memory to feel the pitch difference and
sometimes use "silent singing" to feel the pitch difference. In either
case, with body memory on your side you can reproduce pitches a lot more
precisely. This is an argument in favor of rote learning and practicing
a lot.
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