We often run into the deployment tool being blocked due to minor DLL differences between environments. For example, we may upgrade the dev enviornment to a new hotfix to test, but then we are no longer able to deploy with the deployment tool until production is also upgraded with the hotfix, which can many times take time until the customer signs off on upgrading production.
I created a PR (here: PR:1653) using a globalsetting to SkipCompatibilityCheck. If that's worth considering, it would be great to have that approved.
However, it could be implemented using other settings instead, or possibly with a warning rather than a blocking error. But, I hope that this doesn't get lost in becoming a big feature. We simply need to skip that check since we're aware of the differences and typically don't mind deploying with minor hotfix differences.