I have a 2001 LX470 that I just purchased that originally had the ML non-nav system. I am replacing the amp as all of the speakers turned to dust so wanted to replace those with aftermarket speakers. Now however I get this same antenna behavior of 4 inches up, but the blue wire from the head unit is plugged into a blue wire on the harness. Do I need to jump a wire in the old ML plugs that are no longer in use? Does anyone have any interest in an old ML amp?
I'm not sure I fully understand the question, but let me tell you what I figured out. I've done three of these. The one that would be most comparable to yours is my current LC, an '02 where I did a full nav system delete like it sounds like you did. The other two were an '00 non-nav and an '07 nav delete. In all three cases, I removed the factory amp and installed an aftermarket amp in it's place.
There are two scenarios for the antenna depending on whether the head unit you choose has a dedicated power antenna lead or not - some do and some don't. The Alpine's that Ive used have seperate power antenna control, but the Pioneer in my '02 does not. I don't know if that's across the board with all Alpine and Pioneer models or if it's specific to the models I chose.
If your head unit has a power antenna wire, then you'd connect the head unit's power antenna lead to the harness adaptor wire for the power antenna. In that case, the antenna extends when your head unit is switched to radio mode, but retracts if your stereo is switched out of radio mode to something like a streaming mode. My recollection is the antenna fully retracted - never had the 4" chubber you're describing. Separately you'd have your head unit's amp controller lead connect directly to your new amp to power the amp on/off whenever the head unit is on.
If your head unit does not have a separate power antenna lead, then you have to steal the signal from the head unit's amp controller lead. In that case, you'd connect your head units amp controller to both your harness adaptor and also to the amp. The Pioneer unit I put in my '02 lacks a power antenna lead. My antenna fully deploys any time the head unit has power, but if I use the antenna up/down to retract the antenna, it will only retract enough to give me that 4" chubber. It does not matter what mode the head unit is in, radio or other, and the only way to fully retract that last 4" of the antenna is to manually turn the head unit off. In my Pioneer's case, it's by holding one of the buttons on the touch screen for maybe 3 seconds.
Hopefully I answered your question.