Yes, in the current jetBook firmware there isn't any real difference in how these two formats are displayed. That may change with the next firmware.
As for which one to use for reading, use whichever format you can obtain. If both formats are available, I would go with epub. Going forward, epub is based on standard XHTML and CSS and is not proprietary. It is also capable of nicer formatting than mobi, assuming that the reader software fully supports both formats.
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