productivity measures that focus on units of time or labour are anti-agile - they are anti-knowledge work generally as you've pointed out.
any project should be measured by effectiveness not efficiency. efficiency can only be assessed when the following are known and the causal relationship between them is also known:
1. Outcome required (customer value)
2. Solution / Product
3. The means to deliver the Solution / Product
Even in those cases, there is still some uncertainty, but you can measure output over time against all the inputs.
in most knowledge projects you're lucky if #1 is known - most likely it is not known or is uncertain. #2 and #3 are not known but progressively refined over the life of the project. only at the end are they knwon.
so all productivity measures are a waste of time.
You're right about measuring value, but it is not delivered value it is customer enabled value. How do you measure it? By quantitatively defined non-functional requirements expressed solely within the domain of the customer.
anything related to measuring delivered "value" i.e. delivered "stuff" aka "outputs" is a waste of time.