Unfortunately we didn't have the resources to properly address all code-signing scenarios in the Publisher when it was introduced and so we went after the most common scenario - a single App Store provision with a concrete App ID. This means that bugs and corner cases are possible, for which we are sorry.
However, we're in the process of revamping the code-signing workflow and we're taking into account precisely scenarios such as yours, after gathering feedback. You can expect the new Publish wizard in a future release.
the Telerik team
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