There is nothing bad in the same bundle ids. Sandboxed apps and non-sandboxed are linked to a different paths. If you sign your online store app with Developer ID (which is definitely worth of) and use sandboxing in both distributions - there will be almost no difference.
Got answer from Apple: distribution builds of Mac apps cannot be run directly anymore. Instead, developers should adopt the Archive Build Workflow in QA1778: How to reproduce bugs reported against Mac App Store submissions for testing the builds that they plan to submit for the Mac App Store.