I wrote that Slide Deck profile. The default quality settings were chosen for extremely specific reasons. Changing the quality level undoes those benefits.
The videos in your shared folder don’t appear to be PowerPoint presentations, which is what the preset was designed to encode. The encoding time with the Slide Deck preset is very slow because it’s making an extra effort to find identical frames to get the file size down, of which there are many identical frames in a PowerPoint presentation. But live-action footage… there are no identical frames. So it’s wasting a lot of time searching for something it will never find. If your exports are slow, it is not because of YUV->YUV conversion (although that does take a little time). The real slowdown is because of the choice to use the Slide Deck preset.
That’s not really how it works. The best thing is to just ignore the YUV->YUV messages. The system is doing what it needs to do to be color-correct, and it’s quite fast at it. It’s not an error; it’s just an informational message. Your input video is YUV and your output video is YUV. Don’t try to force RGB anywhere, like using libx264rgb.
It appears your luck is unusually bad. 
It would have been nice to see a sample of these JPG and PNG images that don’t work uploaded to your shared folder. Then we can see if we can reproduce the error loading those JPG and PNG files into our copies of Shotcut.
An archive function is not necessary if all media is in the same folder or a subfolder relative to the MLT project file. To archive the project, just copy the whole folder to an archive location, and it’s done. See: