Thank you very much for the description. I discussed this with colleagues and at this moment no workaround will be possible. I'm sorry I cannot help you to implement this solution in Skipper.
Usually, using unique entity names is the safest practice, while Doctrine does differentiate between namespaces without problem, this may cause confusion. Having duplicate names is commonly avoided by just renaming the entity, or merging the two tables in question. This can be managed even in larger legacy projects, and usually saves time in the future.