Closing this as implemented in the next release. For now, defining how a microdata property corresponds to a custom field requires that the admin has knowledge of the possible microdata properties and their structure, to enter the relationship manually in a text field in the custom field config.
It is possible to make this easier in the future with some kind of Javascript chooser, but it would take a great deal of work (VaultWiki devs would have to define every possible relationship), and that doesn't seem like the best use of time at the moment. If this is too cumbersome, we may revisit this in the next branch or thereafter.
Now, to get your microdata/custom-field connections to work, the admin must define at least 1 other custom field that has the Microdata field-type. This new field-type allows the admin to set choices for the Microdata-type of each page. The admin can choose a subset of these from a drop-down, and then editors can pick which of that subset is relevant to each wiki page.
Once the current page has a specifically set Microdata-type, the microdata property relationships of other custom fields will be applied, if they are relevant to that Microdata-type. You may set multiple Microdata-types for a page, with multiple custom fields; this results in the 'additionalType' property getting more values. However, properties gained from relationships to custom fields are only possible for 1 Microdata-type at a time.