I believe I may have found a bug in the Knime compare tool (part of the productivity extensions).
When you compare two workflows, the contents of wrapped metanodes is not taken into account. Unfortunately, I use wrapped nodes in quite a few workflows, so I've switched back to the diff command, which is not that easy to use when it comes to comparing Knime workflows.
yes, this was a design choice. It is also stated like this in the documentation. However, we are currently considering including this as well. I will keep you posted as soon as this is changing.
However, the comparing of metanodes (not wrapped ones) is supported.
We are still looking into it. The decision to not compare the contents of wrapped metanodes was made because the purpose of a wrapped metanode is to act like a single node while a normal metanode helps ordering your workflow.
If you use the workflowdiff to check if something changed within a wrapped metanode during development, Metanode Linking would be very interesting for you. A short overview is given here.
However, we will of course keep you posted on the topic.