Nice article. Just bought the Gemba walks book.
There is no doubt that GDP is an imperfect measure in the ways you mentioned and in other ways. There are a lot of other theoretical measures (like you suggest GDV), but it may still be one of the best we have. Another measure that I have seen economists use is Total Factor Productivity and with that metric the productivity paradox still remains.
Side note - You can see some of my notes on 30+ potential explanations for the productivity paradox in this Google Doc I created:
https://docs.google.com/document/d/1oLsIAK7JMNjhj_yYE8frwolmcKQZA3vXqIiB4L4sdAo/edit
The more I've explored it, the more different credible explanations I have seen.