Ok, I got this. I hope there is an easier way, but here is what I did (may be helpful for others):
First, you will need to have a keyboard and mouse plugged into your batocera box. You will also need a second PC - preferably a laptop.
SSH into your batocera instance from a second PC and do this:
# export XDG_CONFIG_HOME=/recalbox/share/system/configs
# export XDG_DATA_HOME=/recalbox/share/saves
# export DISPLAY=:0.0
This should launch dolphin-emu on the batocera box.
At this point, I did not have a mouse-cursor. The mouse works when hovering over things, but nearly impossible to use without having a visible cursor. So, the rest of the instructions assume that you also don't have a mouse cursor.
Press F10 (or maybe it was F9 or F11 - one of those). It should bring up the File menu.
Navigate though the menus until you get to Config. Press Enter.
In the Config dialog, navigate to something like "ISO Directory".
In that panel, add the GameCube ROMs directory. It should be something like /share/recalbox/roms/gamecube.
Now, the game list should be populated. You should see all of your GameCube games in there. (If you have games subdirectories, you would have needed to check "Include Subdirectories" in the previous step.
Now, find "Legend of Zelda - Twilight Princess" in the list. Here you will need to hover the mouse around and click in various places until you are over it (since the cursor is not visible).
Right-click over "Legend of Zelda - Twilight Princess" and click "Properties".
From here, you find the tab with "Hyrule Field Speed Hack" and check it off. Click "OK" and then exit.
Now, you should be able to play with that new setting.
I am still baffled about where this setting is stored. I did not notice anything different.
I will also add that it appears that manually updating:
did not have any effect.
If anyone knows an easier way to help others, that would be great to add here. Otherwise, at least this works.
And the difference is night and day. You should know when the hack has been applied when you try to go around Hyrule Field.