They are certainly cannon, as they are mentioned in the game and the game is 100% cannon.
The Commonwealth has been mentioned numerous times in the main game and the DLC... given its proximity to the Capital Wasteland, it would be easy for some story carry-over, and Bethesda likes to hint toward future projects, so most people assume The Commonwealth is the site for Fallout 4.
Broken Banks is mentioned just the once that I know of, and is said to be South of Point Lookout, which is South of the capital wasteland... I assume it a somewhat developed area of North Carolina or something, on the water. Probably not a mecha or anything, as it would be mentioned more often.
I don't remember the "religous institute" thing... I'll have to look that up.
Anyway, Bethesda loves to tease future developments and games in their projects... Cyrodiil was mentioned many times in Morrowind as being in trouble and the like, and then we got Cyrodiil as the main location in TES4. I have no doubt we will see these hinted to locations someday, somehow, given the time and interest levels in Fallout stay where they are.