I have been driving myself absolutely insane by using Window -> Developer Tools in Beaker Browser. This is the set of dev tools for beaker itself! This is COMPELETELY NOT HELPFUL for developing SAFE apps using the DOM API.
I am not sure how else to get the actual page dev tools but I know at least one way. I am using right click anywhere on your app page and select inspect element. This brings up the actually relevant dev tools.
I hope the docs/guides will be updated to reflect this note. I wasted a bunch of time because of this.