The intended order of season 10 did indeed plan on having Merlin's Shop of Mystical Wonders as the 3rd episode. Due to production difficulties, however, the episode was only ready to air after the planned final episode, Diabolik, making Merlin's Shop of Mystical Wonders the final episode to be aired during MST3K's original run. The way that TMDB chooses to order episodes (different shows will have different orders between air dates, production, media releases, etc. and so it's good to have one be the 'main' ordering to keep things consistent) based on the air date. This means that the present ordering is the correct one in terms of the site's rules. The intended order of episodes - the order they were produced in - is available in the 'Production Order' episode group. Episode groups can be seen under the 'Overview' menu. If you happen to be having issues with the main ordering because you are requesting metadata for a home media server, you may be able to choose the 'Production Order' episode group for the display order (assuming such a thing is supported).