I believe it may be due to the amount of SPIII ATF required, and its
cost.  It may require 8 or so quarts, and this ATF is not an
inexpensive as motor oil.  I would be very careful to make sure,
however, that they do indeed use the correct ATF.  If they don't, it
can cause tranmission failure.

For $89.95 labor, I'd suspect you're getting a transmissin flush instead of
a drain and fill.  If not, you should take your business elsewhere.  (Check
around before you do.  For all I know, $180 is the going rate for an hour's
labor in your area.)  

As for the $8 in shop supplies, it's unfortunately a standard in the
business.  Rather than increasing labor rates or parts prices, shops began
including shop supplies.  It is what it is, and it won't change without
legal intervention.  Just be sure to compare apples to apples-- know what
the shop supplies charge is up front prior to the work.  Any reputable
place should be willing to give you this information.

If your fluid smells and looks good, you shouldn't need any more than a
drain and refill and replacement of the filter.