@Black Heretic: I have some rough estimates on a few of the DLC levels, but I haven't documented them and don't remember most of them. What I can tell you is that they're developer times with some seconds added on top of it to make it slightly easier. Comparable to A+ in Super Meat Boy.

@Doctor Why: I was referring exactly to the level slot you mentioned (4th level slot in the 2nd row of each of the worlds, plus 2nd slot in World 6), so they're "leftovers" in the end, thanks for the info.
I take the opportunity to ask another question: is there any way to know the "exact" coffee times? I have already beaten them all, but I was trying to manually determine the thresholds for each level (by replaying them multiple times), to help people estimate how close/far they are from beating them. However, the manual process ended up being too long/cumbersome when I tried, so I temporarily gave up.

@Black Heretic: Also forgot about one specific case of World 6 (Beyond The Void): That world doesn't have any component for the spaceship, so the 2nd box in the 2nd row is also locked, because it just isn't.

Black Heretic: Hey, BH Speedrunner here. To answer your question: the 4th in the 2nd row of each of the worlds (except for Crashsite) is probably a misunderstanding. If you want to teleport on Crashsite, you'll see that that box corresponds to the Endera spaceship. The last 2 of the 2nd row are DLC levels (see Secrets of the Entity) and thus require the DLC pack to be played. If you already have the DLC & finished the main story line (e.g. repaired the ship, destroyed Deuriel & got Cpt. Jetsen to do his motivational talk about "dark selfburns"), that's what you collect in the DLC. Hope that helps!

Thanks for replying. I already added a comment in an existing thread but received no response. In short, my question is: even after completing the game, there are still some locked levels in the level selection menu of worlds 2->6, so I wonder if there are additional secret levels to unlock.

@Black Heretic: Hey! Thanks for completing the game! You can ask here, but I think it's probably better to post a new thread in the Community/Discussions section of the game on Steam, so other developers can see it too!