Nabisco is a DSD vendor. It's own sales associates and merchandisers are responsible for ordering and stocking the shelves. These people are on site (in-store) at most once per day (depending on the unit volume of the store and delivery schedules). Data gets funneled to the sales associate to make their own judgement calls about ordering (though they may be on auto-ordering depending on how close of a relationship the store/chain's snack category management has with Nabisco). High volume stores get 2-3 Nabisco orders in a week.
Sometimes there isn't great communication between sales reps and grocery/store management because of how little involvement is necessary on the store's end. As a manager at a full assortment grocer, unless you have a very specific interest in Nabisco, you may not even notice a SKU is out of stock. Reps will hide shelf tags, and increase other product facings to make it seem like they're fully stocked. Unless a customer brings it up to you, you may have no idea. From a data perspective, an out of stock issue is virtually indistinguishable from a slow-moving SKU as the granularity of sales data is usually only at the "day" level (and due to shrinkage, generated inventory counts are unreliable). So a large demand for parmesan garlic triscuits may not be evident for whoever is reviewing the data.
Also, your reasoning is a little flawed. Parmesan Garlic being out of stock does not necessarily indicate it is more popular than other flavors. It indicates simply that they ran out of their allotment, which (for big sales) is usually centrally planned according to production and previous sales figures. Your store could be in the midst of a negative feedback loop, where previous out-of-stock situations deflate sales figures and affect future allotments, which simply makes the parmesan garlic SKU go out of stock before other "more popular on-paper" flavors.
Another way to look at it is that the margin on triscuits is so low (and even lower when on sale), that caring too much about the extension SKUs is not worth the time/effort. As a rep, you'd mostly be worried about keeping the primary SKU in stock, occasionally juggling other stock from store to store when management gives you a hard time (if they even notice). As a grocery manager, you're probably oblivious if the vendor is actively trying to hide the problem.
Some brands that have an owner-operator type DSD model (where the reps actually work for themselves and own their own routes) are usually more conscientious and concerned with maintaining a full assortment. Ironically, they tend to not have as much frontline support as the corporate DSD behemoths (like Nabisco) so they have to work much harder to cover more stores (but at least they reap more of the benefits of their hard work, potentially). These are usually more regional or local products.
TL;DR
Safeway probably doesn't care or doesn't know, Nabisco also probably doesn't care. Best way to deal with something like this is to submit something to Safeway corporate that a specific SKU (include the UPC) is always out during a sales period at a specific store (if you can find out the store number, even better). The most direct approach would be to find the Safeway snack category manager on LinkedIn and shoot him a message.
Source: Was a Grocery Manager for Wegmans for several years