There is a drain for the differential on the 2003 Sienna.
I did not have the fill plug, however it is filled through the transmission.
In other words, they share the same fluid.
Draining the differential as well as the transmission pan gets some more fluid out during the drain process, but not a lot of fluid.
However, it is not manditory to drain the differential as it is sharing the fluid with the rest of the transmission....so when you freshen up the tranny fluid, you freshen up the differential fluid (speaking for front wheel drive, not all wheel drive, which has another differential for the rear to wheels).
THIS picture shows the location of the 2 drain plugs on my 2003 Sienna........I am under the vehicle (which is up on ramps) looking forward.
I would recommend doing as you are thinking of doing.......do another drain and fill.
Draining the pan gets, at BEST, 1/2 of the fluid......4 quarts.
The total system capacity is 8 quarts.
I also used Redline D4 fluid......but did a full system fluid exchange.
What you are doing will work......you just need to do 2 or (better) 3 fluid drain/fill.
There is some mixing of old with new fluid in the process, which is why 3 times is even better......with some driving in between each time.
The reason you only get about 1/2 of the fluid when you drain the pan is that the torque converter is still full of fluid.
Even removing the pan does not get much more fluid.
They do not put drain plugs in torque converters in most vehicles.....They stopped doing that some years ago.....
The advantage of dropping the pan is that you can do a visual inspection of the particles that the magnets have caught......it should be a fine silt.....chunks are bad.....and you can clean the magnets and pan.
The other advantage is that you can replace the filter, but the filter in the 2003 Sienna is just a nylon screen.....so not really much gain there.
THIS picture is what the old fluid looked like next to the Redline D4.
The old fluid had about 30K miles on it and I don't know what brand it was.
As a side note...you could use the same fluid, Redline D4 to change the power steering fluid.
I unclipped the power steering fluid resevoir from the inner fender and just dumped it into a shallow pan.
No need to unhook any hoses.
I refilled it with fresh ATF, ran the motor, turned the steering wheel back and forth and then repeated the drain and fill.
The owner's manual calls for the same Dexron III ATF fluid.
The OEM seemed to not have the red dye in it, which has caused some confusion.