Unsually brake situation

Usually your squeel problem is solved by applying shim grease to the thin metal shims that are on the pads, toyota has two backing plates (shims) on their pads. Usually the one on the pad has verticle slots cut out and the one that rests on it is solid...you only need to grease the back of the pad and the back of this first plate...just don't overdo it...and also..don't under do it...a light coating is fine.

Also every brake job I do gets the slide pins cleaned and regreased with grease designed for that app. I also use a modifies toothbrush to clean out the bracket slides...you'd be surprised what you can get out of their even on the first brake job. Bearing grease is a no no, I use raybestos brake parts grease, I forget the exact name of it but it's meant for the slide pins.

You should not use such hard pads because they may last (lifetime warranty pads are NO NO) but they do so because they wear out your rotor instead of them wearing out.
As to taking it to the dealership, if your car needs an alignment then it needs the alignment, you need to get it done

BUT by no means does the dealer have to do it. Find a reputable shop around you, I recommend the dealer because they will get the job done, and if they don't, there is always someone over someone you can go to...maybe as high as the toyota comp. themselves if the problem can't be resolved. There are exceptions to work quality at dealerships though...so ask around.

If you take your car to the dealer, and they recommend an alignment, you don't have to let them do it. They will prolly recommend a slew of things for your car you can do yourself and/or get done cheaper somewhere else. I prefer the dealers cause in general the work quality is more insured...however...this is not always the case...again ask around first, you will most likely be able to find a shop that is as good if not better than the dealer who can get it done for less...after all...ind. shops don't have so many higher ups to pay, so they charge less for labour.

If your suspension angles are not correct your going to suffer premature tire wear and reduced handling...well...theoretically reduced handling...since these aren't fully built race cars you will prolly not notice (aside from a pull) to much if your caster and/or camber spread is .5 degrees vs 0.0 spread...any way your tires will prolly wear funny.

Any way as to the grinding, might it be a characteristic of those rotors and pads?

Can you take your wheel off and visually inspect the brake components? Check them out if you can, look for spots on the rotor that has been excessivly worn, such as on the top of the rotor...signifying a rock being stuck inbetween the rotor and caliper, check every component, you really need to take it all apart if you are hearing an abnormal grinding.

I have not used cross drilled/slotted rotors so I can not comment on their sound...the squeeling though, especially under light braking...backing plates (shims as they are also called) and lack of grease on them is first suspect.