So to the best of my knowledge, knitr (really, pandoc) is simply overwriting the old document with a new one every time you knit. It’s interesting and to Word’s credit that it picks up the new underlying file, but I think that’s entirely on the Word side and nothing to do with RStudio or knitr.
If I’m understanding you correctly, you’d like to have the same docx file open simultaneously in both Word and in some sort of XML editor or text editor and make changes to the XML? That would not be quite the same scenario, and it might be ok or it might be disastrous — I think you’d need to carefully test it to find out.