[JKT]

You can use the same trick as the one for OmniWeb's Workspaces - navigate to your OmniFocus folder in ~/Library/Application Support/ and drag the Perspectives folder to the right side of your Dock so that you have easy access to it. When you want to launch in a specific perspective, select it from the folder in your Dock. OmniFocus will then open in that perspective (you can also use it to open different perspectives in a new window while the app is already running).

Edit: However, it would be better if there was a built-in UI for doing this (e.g. that you would invoke by holding down shift when launching to present a perspective picker).