No I never did find a solution. I've asked a few Esri topology folks, and they say the version changes tool is not intended to be used with topology. Someone suggested Data Reviewer, but we don't have the budget for the additional extension, and one Esri employee told me that you would have the same problem.
The only partial workaround that we sometimes use when feasible is to have our tech make edits and before he/she validates topology we use the version changes tool to review the edits, then the tech validates topology, fixes any remaining errors if found, and then we post to the parent.
You say the changes are "accumulating over time". If you do a reconcile/post, then the two versions should be synchronous again, and you wouldn't see anything in the version changes tool until you start to edit again.