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I'm not aware of this limitation. I have successfully published data sources with cross database joins to Server (and Tableau Online) and the automatic refreshes work fine. You may be thinking of data blends which cannot be published (though the individual data sources can be published and then blended in any workbook using those sources).
I have the same issue. I have a spreadsheet joined to a teradata table. I am constantly adding new data to the spreadsheet. TWhen published on the server tell me that the data is refreshed but I do not have any of the new data from the spreadsheet available in Tableau. It works on desktop but I can't be manually updating the workbook every time the data updates. And I can't use a blend because the teradata table is merely functioning as a look up table (I am not pulling summary data out of it). Any suggestions?