I just posted this in another topic funnily enough, yeah this particular app is hardcoded so you need the Alfred 2 folders:
EGGPREFS="$HOME/Library/Application Support/Alfred 2/Workflow Data/carlosnz.eggtimer2"
EGGWD="$HOME/Library/Caches/com.runningwithcrayons.Alfred-2/Workflow Data/carlosnz.eggtimer2"
Which are ~/Library/Application Support/Alfred 2/ and ~/Library/Caches/com.runningwithcrayons.Alfred-2/. If you have those folders it does work with Alfred 3, as I use it all the time.