I'm doing the same fluid changes on my 2012 X35i this week. The only difference between our two vehicles is that you have a 6 speed ZF and I have the 8 speed ZF trans, I believe.

The transfer case fluid is dealer only, and cost like $75 a liter. Expensive stuff.

The front and rear diff takes GL5, which is common stuff. I got, after reading many posts regarding the diff fluid, the Red Line 75w-90 synthetic. They are like $17 a quart, and it takes 3 quarts to do both front and back.

The trans fluid....that's where we differ. The fluid for my 8 speed runs like $80 a quart from the dealer, but I got the ZF fluid from FCP for like $20 a quart. Big difference in cost when you have to buy 7 quarts.
As I understand, and you would have to verify for your 6 speed, is that you can use the stuff that Ford used in their ZF 6-speed tranny...I believe the stuff is called Mercon SP, which only cost like $8 a quart.

So the quote from your Indy seems a bit high, unless the costs quoted include the work to put them in.

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03 Z4 2.5i
12 X5 35i