Hi again Hugh :]
As I mentioned in your ticket, SmartAssembly choosing the wrong dependencies is indeed a bug. It is unfortunate, but as I understand it, this behavior is kept as it's important for applications running on different frameworks.
When this behavior causes issues, the workaround is to use the MandatoryPath. However, you're right that it would be a good idea to warn users that a different dependency was used, regardless of whether or not it causes any obvious errors. I've created a feature request for this (with reference SA-1593). Thank you for the suggestion and again, sorry that you're experiencing this issue :/
Red Gate Software Ltd.