we can publish data source to server, if you used live or extract.
some bigdata will take more time.
we can use the twb format when publish to server is best, because if you use twbx then dataconnection also publish.
2. This is a more complex question. It depends on your server hardware and OS, the number of Tableau processes available, other Tasks that are executing when this particular refresh is happening, data source itself can be a source of issues (are you refreshing during a db maintenance period, batch processing, etc.).
3. It's a workbook so it would be a .twbx. A .tde is a data extract only, not a workbook.