There is a workaround, though it's a bit fiddly, and requires that you're using MPC:
Ensure that you have "show all formats" enabled. Copy the video link as always, then select the video stream you want (298 or 299) and click the "copy" icon (looks like two sheets of paper, between 'play' and 'reload'). Open MPC, click "File --> Open File..." and paste the URL into the upper field. Don't click "OK" yet. Return to SVPtube and select the audio stream, will usually be called something like "Audio (mp4, medium)" and will also be a strike-through font and also copy it. In MPCs open-dialog, paste this into the lower box ("Dub") and now click "OK". This will play the selected video stream with the audio stream and should work.
As I said, it's a bit fiddly...
I really hope we'll see direct support for this soon (even though I've only just discovered SVPtube, I already love it). It should be relatively trivial to add the format definitions to tell it how to handle and treat the streams. Looking forward to it