Hello,
Interesting. Are you inserting the text boxes into the google doc as a drawing? ( menu> insert>drawing - this is the only way I know to have text boxes land in google docs) If so then yes you are right, I don't believe Autocrat will work because the drawing on a doc will be processed as an image and Autocrat will not merge inside an image. I don't know if this will be a solution for your question but Autocrat can merge inside table cells, so if you go to the menu >insert>table; you could for example have the image in the middle table cell and the merge tags in the cells around it.
You could format as needed by merging cells and changing the color of the table outline to be white if you needed to. Hope that makes sense.
Or you are also correct that a slide template is an alternative that would work with text boxes.