Possibly related to the chroma upsampling method used during a colourspace conversion? (I don't know, I've never used MPEG Streamclip). Basically, if you're converting video that uses the YV12 colourspace into YUY2 or RGB, the chroma needs to be upsampled differently depending on whether the video is progressive or interlaced.
But then, I don't know why enabling this option would make the video larger.