In the context you mention (microwaving something in water, e.g. instant oatmeal) I have usually seen two distinct options:
- Boil water in a kettle or on the stove, and add the boiling water to a bowl containing the product.
- Add the product and cold water to a microwaveable container and microwave them together.
But if the instructions really do say to put boiling water in a container and then microwave it, I would first boil the water and then put it in the microwave to cook further. Boiling water in my experience always means "water that has been heated to a boil" and not "water to be boiled" as in cooking oil.
If you are able to share a specific product or recipe that calls for placing boiling water in a microwave to be cooked further I would be interested in seeing it.
Response to your edit: The phrasing they use sounds a little strange to me. I would not expect to read "Place 200ml of boiling water in a saucepan;" instead I would expect "Bring 200ml of water to a boil in a saucepan" or similar. Perhaps they are assuming you would use an electric kettle to boil the water before pouring it into the saucepan.