The MAS version is much older and doesn't have all of the stability improvements, new features and bugfixes in it that the version from the website has. This is literally the difference between the two. We no longer publish to the MAS due to the sandboxing restrictions which a tool like SourceTree can't get around without limiting what it can do.
There'll be no more updates in the MAS for SourceTree so I'd highly recommend you download our version from the website.
Hope that helps!
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