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Binary values are always stored in the binary store, and this is true even if your nodes are "mix:versionable". So which binary store you pick is completely independent of whether or not you use versioning.
But please be aware that JCR versioning has some usability limitations: older versions do not appear in the node structure is an easily accessible manner, but rather accessing older versions requires using the VersionHistory interface. Also, JCR versioning basically creates snapshots, so it's not necessarily more efficient than if your application explicitly manage its own version structure via copies.
OTOH, if you're talking about federation and using external sources, then you are right that federation does not support versioning. Again, you might want to consider using something other than JCR versioning.