Quick tip: if you need to use the Steam console with Bottles, add steam.exe (if it's not there already) to your program shortcuts. Click the vertical ellipses on the right to show the options menu, then click 'Change launch options'. There is a field called 'Command Arguments'; enter -console and save. The next time you launch Steam with your Bottle, the console will appear in your Steam menu.
Now that I have figured this out, I can downgrade Fallout 4.