I’m the engineer that wrote all the initial replacement algorithms and I currently work on the Instacart fulfillment system. We never have designed or even considered a system that would attempt to profit off not found items, that’s insanely anti-customer and unethical. We do suggest items on the storefront, pre-purchase, but our substitution recommendation system is entirely driven based on any specific requests from you (that order or previously) and a collaborative model driven by prior replacements.
We are also working on better ways to collect preferences from folks; I’m not sure when any of that would be going live.