Well, the updated Workbench is one of the many features OS 3.9 brought with it - it wasn't intended to be used with 3.1, so it's only natural that it will bring with it a bunch of dependencies and potential incompatibilities. The simplest way to get the OS 3.9 features is to install OS 3.9. I'm sure you can find an image of it somewhere though if you've no intention of buying it...
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