When you populate a table in a word doc from a repository search it treats each entry found as a row of the table. I don't believe that it is set up to pull multiple values from a metadata field within a record.
Coders out there may now how to combine the values with a custom script. But since I don't write code I am only guessing.
All the word docs I update, I pull from a database table. You could attempt to set up a temporary database table to work off of. After your search, you would have to do a For Each activity that would look at the search result and put it into the database table. For multiple values in one field you would either have to have all the values combined into one field, or create an entry for each value.
The you would have to search the database table and use those results to populate the word document.
If you don't want the database table to grow, you could do a custom query to delete all the values at the end of the workflow.