The article is actually written specifically for the BI Publisher Desktop. A close following of the instructions should result in success.
For use from the JDE application your CNC will need to deploy to the JDE Enterprise server in a similar fashion but the JAR file and xdo.config file locations are different than the BI Publisher Desktop.
Note that the blog post mentions a QR font from IDAutomation. It is a commercial font. I have used it successfully along with a few other bar code types from them. Their fonts and encoders have been reliable and worth the price in my opinion. There may be a free or open source QR fonts/encoder out there. You would need to use the same approach to integrate with BIP i.e. compile the encode into a .jar file, copy the .jar file into the BIP Desktop JLIB, upload the font TTF files and then add the fond to the xdo.config file.