"... it'll never hook on a surface irregularity and it'll just squeal like it was designed. So it should always be positioned at the top."
That may 'sound reasonable', but that's not the way pad wear squealers were designed to work.
Remember, the intended function is to make as loud a sound as possible at the first contact between squealer and rotor.
If the the contact edge of the squealer is positioned at the TRAILING edge of the pad, it will make a very slight scratching sound as the rotor first contacts and sweeps past it ... all there is is the gentle pressure of the squealer, acting like a leaf spring, rubbing against the rotor. This small scratching may be totally inaudible to the driver.
If the edge of the squealer is positioned at the LEADING edge of the pad, the edge of the squealer will 'dig into' the rotor, bend the squealer until it releases, dig in again, release, etc. many times a second creating a high-frequency resonance and what should be a horrific racket, at least to the discerning driver.
So for the FJ, both front and rear pads should be installed with the squealer at the INBOARD position, and with the squealer positioned at the BOTTOM of the caliper, so the squealer tends to be pulled TOWARDS the pad when it first contacts the rotor.
That way, first squealer>rotor contact tends to cause the squealer to dig in and cause a major unmistakable acoustic oscillation that screams 'BRAKE PROBLEM!!'.
The squealers are thin, hardened stainless steel and won't break off or get sucked between the pad and rotor.
It is a little odd that the Toyota FSM doesn't mention squealer orientation, but I believe the multi-language installation guide that comes with OEM Toyota pad sets does.
(I recently replaced the original factory-installed Sumitomo front pads on my '14 at about 65K miles, and the squealers were oriented inboard/bottom, as described above.)
Here is a YT video sponsored by Advics (A Toyota OEM brake pad supplier) that focuses specifically on squealer orientation:
orientation of sqqe=ueeler on brake pads - Google Search