Could GM author moves to establish the puzzle, perhaps fabricating clocks of some kind? That is, is the distinction found in the structuring of the breach in security puzzle?
How could that be workable? Either the GM authored a 'security breach' story, in which case the parameters of that narrative are going to be all of a piece and hang together, or else the players and GM together establish, via action declarations and outcomes etc., the concept and parameters of a security breach. A mix of the two isn't going to be viable because the GM's conception is going to 'go off the rails' as soon as a player declares something that breaks one of its hidden-from-the-players assumptions.
So, yes, you can do a BitD type of thing where someone, maybe the GM, introduces the bare IDEA of a 'security breach' (probably part of an info gathering move in BitD). Once the players think of an approach and some appropriate starting position is determined, then they make a move which establishes the success of "trick the sister into giving us the password" can happen, and a clock being established would certainly be a likely way for the GM to handle putting some pressure on the PCs "once this clock ticks down the sister is going to get suspicious and figure out something is up." It might simply be established as a basic aspect of the situation, as a response to a 'success with complication (4-5)' result, or as a devil's bargain condition. But this is more how BitD employs its tools to produce 'forward drive' in the story, creating tension, etc. In a PbtA type version of this there would be some sort of soft move announcing badness to come, which is pretty similar. You could certainly also use a clock (or a Skill Challenge) and that could be established even in a classic style of play.
So here I am not positing a rule whereby mechanics are or can be made silent. I'm envisioning the possibility of lacunae, i.e. cases not covered by mechanics. Where rules do not extend, what happens?
Well, as I have pointed out many times, PbtA games don't have this issue AT ALL, they rest upon a completely universalized process which handles any possible situation in the same core way (at least the ones I'm familiar with, I guess this is not utterly mandated by the design). So, thinking about BitD, it works within the paradigm of the structure of its given milieu. Obviously if the game went to something like "Doskvol is completely destroyed in a cataclysm, survive in the death lands beyond!" then its info gathering, downtime, score sort of core structure would basically fall apart. Not that its action mechanics and similar tech couldn't be applied, but this game, and TB2 as well, rely on a fairly known predictable cycle of action. I think we can see that, yes, some games can have holes in them, or limits they can't go beyond. I don't think that has a lot of significance beyond understanding that each game codes certain assumptions into it.
One way to address the possibility of lacunae is to say that there are none. A question still on my mind relates to the focus on action declarations. Simulationist rules often extend beyond action declarations to world processes. World processes could fall outside of feasible action declarations... so can I count on their being covered?
Covered by what? As I keep saying, something like a PbtA can be completely universal. Imagine Traveller truly played in a completely PbtA universalized way. "OK, I navigate the ship to the jump point and plot a course for the nearest world where I can refuel and trade." This move 'Navigate' triggers a generative process, as move-specific rules that determines where this nearest world is and its relevant features. I can build basically all of Traveller in this style! Everything! The Steward move can include rules for what sort of people try to buy tickets on your ship, are they hijackers, refugees, etc. I mean, as much as is desired of all this can be left to "GM decides this part" or whatever. Maybe if you navigate badly you could end up at a Class D port with no Lhyd, or frazzle your drive, or misjump, etc.
But note that this sort of rules doesn't have 'lacunae' of the sort you seem to be looking for.
@pemerton's issue with planetary exploration/operations doesn't apply because outcomes are GENERALLY just "things go the PC's way" or "things basically go the PC's way, but there's a hitch", or "you get exactly what you want." His "does the ground car make it to the base, and is the resulting situation favorable or not" gets resolved. There's really no holes there, because these are very generalized sorts of outcomes. At most a game like this runs into a situation where "it sounds like move X is triggered, but the move-specific 'chose X, Y, or Z' rules don't quite make sense in this situation." I suspect that is always a bit of sub-optimal move design, but I don't see how introducing a non-move-based subsystem fixes that.
A possible example might be where in DW players want to know what the weather is like, and no one yet has access to Control Weather (7th level Cleric spell) or Weather Weaver (Druid advanced move) so they use Discern Realities or possibly Spout Lore? Discern Realities seems straightforward as they can go with "What is about to happen?" The situation taken to be where we are now (say, in these foothills). To give Weather Weaver meaning I would likely want to read "about" as implying "in the very near future" in parsing the rule text. If it's Spout Lore then it's accumulated knowledge amounting to something interesting and possibly useful (10+). Either way, it seems like GM has to decide what the weather is.
GM can decide, but the principles of the game actually decide what it means in play. This is how narrativist systems work. You want to insist on some simulative principles as some necessary core, but narrative games don't need that. They have a core, which is the actual agenda of the game in question. DW; it is raining because this increases tension and is described as, say, 'give them an opportunity with a cost' or whatever it works out to be. Its that simple. If the GM is following the RULES of the game, and in these games this stuff has rules-level force, then there isn't a need for any charts and tables and whatever process. You can still have them, and many narrative games do have additional 'auxiliary' mechanics for various reasons, but they fall at the 'fourth layer of the Onion'.
In a simulationist game there'd often be rules for deciding the weather (I'm thinking of the Balazaring Weather Table in Griffin Mountain), but DW lacks that. If they've succeeded on their checks (7+) it doesn't seem quite called for to treat it as an opportunity to introduce badness. How does GM decide what to say? (Or supposing they turn it back on the players, how does player decide what to say?)
Pure principles. 7+ on some check, things are favorable to the PC in question, but there's some complication or drawback. In the case of the weather, maybe its "the rain will hinder guard patrols, but the steep sides of the swales become hard to climb, and they can flood suddenly, making the terrain more difficult."
