I had the same problem when I installed the Navigation system in my 03 LTD. needless to say that after carefully studying the diagrams for the 03 and the 05 the conclusion of the why the antenna goes up is because the wire that was used in the 03 to activate the antenna relay was hot only when the radio option was selected (AM or FM). in the 05 and later, this wire is hot all the time (as long as the key is in the acc or on position) to power the amplifier that is used with both the radio and the navigation voice. My solution to the antenna problem was to interrupt a line with a switch. this allows me to raise or lower the antenna at will. The wire that I interrupted is the wire #13 on the Head Unit connector R4 (20 pins). I'm attaching an image for illustration of the R4 connector. (I do not remember the color of the wire). I hope this helps you solve the problem.
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