Re: Word template content controls missing from Flow
This appears to be a bug in the connector. If you save your .docx file as an XML, and navigate to each of your template inputs, you should see something like this:

Each of the w:id values correspond to json dynamicFileSchema IDs in the Word connector.

I have 4 ids in my template file, and the connector only finds 3 by default. In the preceding image, I've manually added the additional id that was missing, after verifying I had the right id in the XML. I saved the description.json, rezipped the flow and respective files, then attempted an import. The import completed, but failed. When I opened the flow, the dynamicFileSchema was in the flow, but "not found."
I don't know of a work around at this time other than than to simply not use this connector. Maybe generate an HTML document instead?