I think from an engineering perspective it doesn't feel like a debunking. Nothing we assume about the bloom filter has been fundamentally changed. I think that might be the perspective of most people in here.
At the end of the day, this is primarily a formal result with few direct implications on practical usage. As I mentioned in another post, I tried to make it more relatable to an engineering audience, but it's possible that I may have buried the lede somewhat. However, I still stand by the statement that the title is not incorrect, at least if only from a mathematical perspective.
Good point. The main Bloom filter I use at work is 8 million bits in size, and at that scale, it does seem completely negligible whether you account for bits being selected by multiple hash functions since the odds of that happening are so small. We could add a few bits to the 8 million to correct for the error, but that's not meaningfully changing anything; it's just a drop in the bucket.