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I can't say how your dealership will react, some are more mod-friendly than others. But the issue with the whining noise is thoroughly documented in the TSIB and was almost certainly present before you installed the Navtool.
On the other had, it looks like the TSIB installs the noise filter back near the auxiliary jack; you need it inline with the navtool, so you'd have to move it after the dealer is done. Perhaps it might be easier to buy and install the filter yourself, either the one in the TSIB or a generic ground loop isolator like the one sinister2c recommended.
I made an appointment today at 5:30 at keyes lexus. They have been good to me so far, hopefully they wont even notice my little upgrades =) Ill let you guys know how it goes. Thanks for all the input.