Food for thought... I was just working on installing a stereo in a Prado I imported and noticed something. Which Metra harness are you using? I'm looking at the Metra 70-1761 for 1987 and newer Toyotas. The packaging doesn't include a pin diagram, but the color coding shows blue for the power antenna and blue/white for the amp turn-on. When I look at the connectors, there is a short blue wire looping back to the connector and joining with the blue lead you'd attach to the amp switch and/or power antenna. When I think back to my 2007 LC (head unit had a separate power antenna wire), I'm pretty sure I used a different Metra harness, the one designed to bypass the factory amp (#70-8116). I'm wondering if that could be an easy place to investigate.... Is maybe the Metra connector sending the amp on/off signal through what the factory is expecting to be a power antenna channel?
FWIW, I was looking again at the EWD diagram for the radio both with and without the amplifier and I don't see any connections between the amp and the power antenna. As best I can tell, the circuit for the power antenna is limited to the radio connecting to the Auto Antenna Controller Relay and then the power antenna motor itself. This suggests to me that removing and replacing the amp should not have a direct impact on the power antenna and instead it's a matter of tracking down the path between the head unit and the Antenna Relay. Maybe it's this Metra harness Issue. If not, I suppose if you could identify the Antenna Controller Relay, you could directly wire your head unit power antenna lead to the relay.