No, Reaper plays video in two ways, either with what the system provides, which on Windows are the Video For Windows codecs and Direct Show stuff, or the FFMPEG playback libraries.
The safe route is to use Quicktime MJPEG A, which MPEG Streamclip has aboslutely no problem creating. You do need to have Quicktime installed, so MPEG Streamclip can use it.
Test your workflows before you commit. Don't wait until you NEED to have it work.
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