Why is this brake rod threaded with adjusting nut if pedal is apparently not height adjustable?

I'm not a technician.

The extra sensor ("stroke sensor") is a potentiometer used to judge the speed at which the pedal is pressed - sudden braking tells the Skid Control ECU to use friction brakes rather than waiting for regen to kick in. Its position can be varied a little as it's mounted with slots rather than fixed holes, but the range of adjustment will limit what you can do. It needs to be adjusted so that the output is 0.8 to 1.2V (as seen by the skid control ECU - you need the Toyota scan tool to do this) when the pedal is at maximum height. If it's adjusted you need to reinitialise the Skid Control ECU - again, this requires the Toyota scan tool.

The stop light switch is threaded but it doesn't look like it has a lot of range of travel.

The standard "reserve distance" (to the actual floor, not the carpet) is 104mm (4.1"). The height at rest is supposed to be 138 to 148mm (5.4 to 5.8"). I don't think you're in any danger of it hitting the floor if you only move it by an inch.

I don't see why you couldn't move it closer down as long as it doesn't hit the carpet, with the proviso that you likely need the scan tool to recalibrate after adjusting the stroke sensor.