This is intentional, to allow the creation of e.g. buckets, where it is crucial to keep slots empty.

I meant that the pattern of the items assembled by the Mechanical Crafter doesn't seem to matter. instead, the position of the inputs is what seems to matter. As far as I'm concerned, the setup in the image above should craft a flywheel.
Perhaps introduce some method of marking empty slots so the above could work without breaking the bucket recipe?
I honestly thought that I could make my setup more easily this way.

Huh, I never considered trying it that way, but it would be great if it worked.

From what I understand you're trying to pre-assemble items into certain configurations, and then combine those grouped items into the final item? So if you were to make a ladder you might have two 3-tall pillars of mechanical crafters a couple of blocks apart, and a horizontal line of mechanical crafters in the middle joining the two (making a 'fat' H shape, possibly 5+ blocks wide).

When running the system the 3 columns of sticks on either side would be assembled vertically, and each brought towards the center, possible traveling numerous blocks. Then if they 'sandwiched' a single stick in the middle they would combine to craft a ladder.

Unfortunately depending on how the devs designed the mechanical crafting system I'm not sure if this would be possible to implement without a large overhaul. It would require the crafting to be entirely item-position-centric, rather than using the location of the crafting blocks (as it presumably does right now).

We could add a second type of cover that does not count itself as a slot, but simply relays the items over to the next crafter. I'll look into it, thanks for the suggestion.

One tricky thing to watch out for would be if (once you take the relay crafters into account) you ended up with two items in the same slot…

On the other hand, that could potentially become a feature with some “Reality-Defying” late-game crafting recipe (maybe some weirdly spacious storage solution? - not sure if that really fits with the rest of the mod, I just had a thought and decided there was nothing to lose by putting it out there)

Thanks for your suggestion, it has been added to our public submission sheet.