I see no reason to use three different caulks. On the water heater flange I would, and do. use butyal tape only. Same is true on the windows.
The windows I have removed are pretty easy to remove. Simply remove the screws from the inside flange. Have someone on the outside catch the window while you gently posh it outward. Your Bigfoot window flange will look like the one in the photo I posted. It will be sealed with butyal tape. Look closely at it, and I bet you will see where a bad job was done on the factory caulk.