Here is a brief description of the steps I performed. This will almost certainly not work exactly the same way with future releases of the software and may not even be necessary!
1. Start with a fresh install of Raspbian and PIXEL. Do the usual update and upgrade:
sudo apt-get update
sudo apt-get upgrade -y
Start it up and update the Flotilla Dock firmware if required.
curl -sS get.pimoroni.com/flotilla | bash
git clone https://github.com/pimoroni/flotilla-cookbook.git
4. Change into the flotilla-rockpool directory and switch to the Edge branch.
git clone https://github.com/pimoroni/flotilla-rockpool.git
git checkout edge
5. Now for the tedious bit. All the hyperlinks in the examples in the Cookbook are pointing at online resources. We need to change them so that they point at our local cloned copy of Rockpool. Basically you need to go through each of the Cookbook recipe directories (in /home/pi/flotilla-cookbook) and edit the index.html file: change wherever it says 'http://flotil.la/rockpool/' to 'file:///home/pi/flotilla-rockpool/' (note the three /s after file). You could use a bash script to trawl through the whole directory or just open each one manually (Geany on the Pi is a good editor) and do a find/replace.
6. Finally, to make sure all the examples (especially Synth) work correctly with local files, you need to launch Chromium with some extra flags. I created a separate Desktop shortcut to make this simple. Create a file called flotilla-offline.desktop in /home/pi/Desktop
Exec= chromium-browser --allow-file-access-from-files
7. An icon should appear on the Desktop. Run it! I recommend adding Chromium bookmarks to each of the modified index.html files in each of the Cookbook recipe subdirectories. I also added a bookmark for the local version of Rockpool (file:///home/pi/flotilla-rockpool/index.html)