No. CSV output should work on all platforms. When you have finished digitizing your points, click on the "Done" button on the toolbar and a window will open up with the digitized points in it. From this window, you should be able to choose "File-Save As..." to export your digitized points to a CSV file.
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Has the .csv output been replaced with .xml output? If not, is it possible to get .csv output on Linux?
No. CSV output should work on all platforms. When you have finished digitizing your points, click on the "Done" button on the toolbar and a window will open up with the digitized points in it. From this window, you should be able to choose "File-Save As..." to export your digitized points to a CSV file.