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The descrepency is because of the difference between dry and wet fill. Once you fill from the factory (dry) and then drain you never get back all the oil as it gets trapped in valve pockets, gears, bearings, etc.
I understand why you are confused with the service manual procedures. This is because in order to replace the fluid you really need to flush the system to get out all the trapped particles. You can really do this by two methods. 1/ Drain replace fluid, drive for couple of weeks and then drain/replace again. 2/ Drain, flush with high pressure and replace fluid.
Trouble is that in order to flush you need some specialist gear only which tranny shops have. Given the expensive price for the fluid ($20/litre) required I recommend finding a shop that can properly flush and have them replace. When I did mine it cost approx $250NZ to do the work and the tranny has never been better.
Jim
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