It seems very strange to me that they would do this unless they rebuilt the calipers because they had no stock of new and determined that rebuilding needed done instead.
Otherwise, take off working calipers, or not, do them on-vehicle? It does not make sense that any extra time would be spent doing this if not billable. It seems more like something you would get offered at a quick change oil place where they try to upsell a service not really needed, even if they do look nicer as a result.
I don't have a problem with it happening of course (why would I?) but something does not add up. Is it possible that your father replaced the calipers without your knowing about it, before this brake service? How are you certain they are not new or at least newer than the factory calipers? Granted, they wouldn't replace them without billing for that too, but I mean if they were replaced prior to this brake job. Maybe your father did this on his own with some navel jelly or whatever before this point in time? It might be bandits that come in the middle of the night and have this thing about rust, an OCD compulsion to eradicate it on Toyotas.
Wait, let's back up a minute. Do you mean the entire caliper had this coating, or only on the critical areas of contact like the slide rails? I could see a tech using a wire wheel or whatever to clean up the slide rails, slap some naval jelly on, let it sit while getting other parts ready and lube slider pins, etc, wipe it off, and then grease them up. That wouldn't take a lot more time to do if the tech is good at multi-tasking. It's still strange.
You can do whatever you want to your calipers when you service the brakes. I appreciate wondering what they did but your options are basically sand blast with the boot covered or wire wheel around it, clean dust off, phosphoric acid and/or paint... OR you could just slap some moly grease on them, not even necessarily removing the rust, not too close to the brake pads so you don't contaminate them, and let heat eventually turn that into varnish.
I'm fortunate that I don't care if the exterior of my calipers looks rusty on a pedestrian vehicle. I feel the same way about rotors, though I want ceramic pads so my wheels don't get all spotted up and/or eat away at the clearcoat.
