JalviewFileChooser should not default to JVP if only the default opening file has been opened

If Jalview is opened without initially opening a file, the JalviewFileChooser will default to "All known alignment files" as file type, as per comment
https://issues.jalview.org/browse/JAL-4206?focusedCommentId=25962&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-25962

However, if the startup file is set, then this sets the default file type shown in the file chooser as the type of that file. A user launching Jalview without specifying the file in --open would probably want their options open about opening a new file, so the default in this case should remain "All known alignment files". Arguably this should also happen if all windows have been closed.