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Here's my experience you can take from it what you will.
It wasn't Jiffy Lube but a 10 minute quick lube place where the techs
seemed more knowledgeable.
Shortly after I purchased the car with 85,000 miles on it, and was in
for an oil change, they pointed out a transmission pan leak so I let
him change the gasket and clean the screen in their solvent tank while
I watched. When I saw the fluid come out, it looked dark to me so I
went ahead with their transmission fluid exchange. There really is no
"flush" - just a machine with two reservoirs. One holds old fluid, one
new. Two hoses are connected to the transmission cooler lines as and
the engine idles, the internal transmission pump slowly pumps out the
old fluid and in with the new.
Perhaps because I'm a purist, I asked how much fluid would be required
and purchased the genuine Toyota ATF at the dealer which was OK with
the quick lube place. I think it took something like 10 quarts and he
suggested I buy 12 just to be safe. Turns out the exchange has some
overlap. The total capacity is not 10 quarts but that was needed for
the process.
Then I discovered Mobil 1 synthetic ATF and began draining the
transmission pan at oil change intervals to do the change over. I also
changed the differential fluid to synthetic and noticed an immediate
improvement in acceleration.
Later when I began doing my own mechanical work and changed the timing
belt, oil pan and transmission pan gaskets, I found two stripped
transmission pan bolts - that was the real reason for the leak.
The one caution I would add, is that Toyota requires you drive at least
ten miles before performing the final fluid level check on the
transmission to get it up to the "hot" range of 158 - 172*F. When the
quick lube place did the final level check, they just told me to drive
around the block.