From what you say, it sounds like ColourLike is just buggy. Has anyone informed the author that it doesn't actually perform like his instructions say?
Although re-reading the details thinking about what you've said, it could be intentional. It could be assumed to average together every single frame (with every=1) or every 3rd frame (with every=3). That blows...
Although it is not recommended, it might be possible to force it to do what we want by incorporating WriteHistorgram and ColourLike into the same script.
Some sort of For...do loop that counts off each frame, trims one frame at a time, generates a histogram for source and destination clips, applies colourlike to that frame, and then increments.
Theoretically possible, probably crazy slow to make work.