In a business that operates at a scale of 100s of thousands if not millions of bottles sold annually, cents matter and can make up a significant portion of revenue.
With this in mind, there is a huge incentive to get people to buy sooner rather than later and more often. Forcing a small amount to remain in a used up bottle is definitely a benefit to the company even if the product is going to waste. This doesn’t include the cost of implementing something new. I’d imagine a company would do extensive survey based research to understand if the additional customer satisfaction would outweigh the costs/downsides.
If it’s not a conscious decision, it’s a nice coincidental benefit to them.