The reason to replace the water pump and thermostat at this time is that you need to dismount the timing belt to remove it from your engine, So replacing the water pump when doing the timing belt just involves removing about 6 small bolts and nothing else.
I do beleive Toyota dealership should have retimed the injection pump with the dial gauge tool. If they did not use the dial gauge technique then the only difference you had compared to ustaad shop is that you sat in an airconditioned waiting room. The bill of Rs 18K is a little high for just 3 parts and labor. If they did pay attention then you would also have the little mileage sticker on the T belt cover now.
The correct parts list also includes two oil seals - one for the crankshaft snout and one for the camshaft. They are already heat aged at this point of time, just like the waterpump and thermostat valve are aged at this time too. Anyways - your car your money your choice.