The "prominent" dealers you're referring to
(and the one I'm thinking of was the topic of
a Mononoke/Nadesico separation discussion a 
while back) was separating cels/douga that
cost up in the thousands.  Even to purists
like myself who think the parts that make up
the cel should stay together, it perhaps softens
it a little when I see someone who really wants
to own a Miyazaki piece but can't afford to pay
$2000 for a cel is able to buy a douga for
a few hundred and be happy... I'd still rather
see the pieces stay together, but for pieces
that cost amounts that are not easily spent
by many collectors separating the two for
availability (although I think there *was* some
greed involved on the part of the seller)
makes a little more sense.

Separating a cel and a douga (and a genga, which
most likely came as a set ANYWAY since the
seller has all three at once!) when the total set
would probably sell below $150 (maybe stretching
it to $200 at best) doesn't buy the kind of
justification between making expensive
pieces more available.  The seller is just
being greedy.  And I think he/she probably
listed the douga at a higher starting price 
because he/she knew there would be more interest
in the cel, and still wanted to make some extra
cash off the high bidder.

As for Taro selling douga alone: I think Taro
even explained once that they don't separate them,
they sell them as they get them.  I'm sure
that thread is in here somewhere if I remembered
it incorrectly...

Since there are always niave bidders on eBay,
I'm sure the seller will make his extra cash
from separating the matching pieces, and will
probably continue to do this in the future.
At least he/she has lost one potential customer
here...