According to the 4runner service manual from Toyota. The maximum rear axle shaft runout is 1.50mm and the rear axle flange runout is 0.05mm.

I agree which is why I'm having a hard time believing that this axle shaft is so out of spec that I need to spend 2k replacing it. Especially since the only symptom is a small squeak hear and there. At the same time I don't want to "assume" I know more than what I really do and then down the line I have an even larger issue.

Do you have any vibration when braking? If the brake disc wobbles too much or is warped, then you will feel a vibration when braking as the pads move back and forth to accommodate the wobble. If you have no vibration, you should be good too go, as others have said about the run out.

I have no vibration when braking.

There are other options to fix this besides replacing the axle like machining the rotor to account for runout. There are also shims, not sure I would trust them. Both would be more of a bandaid to the actual problem.

To be super clear, your slightly bent axle flange is causing everything mounted to it to also have runout i.e. your rotor and wheel / tire. As your tilted rotor spins it makes the contact surface between the pads and rotor not parallel and dynamic (squeaky). Your wheel & tire are also wobbling although you are not feeling that.

The more runout the more it will reduce your brakes performance, eat up your pads / tires and make noise. We are speculating you are double the allowed.

I think the tolerance is ridiculous and would have thought the caliper could account for some minor misalignment issues but we are talking about high speed rotating parts that need to be parallel to other surfaces to function.