As you say, it's a controversial --and complicated-- figure to determine.
The problem is that there's a big range, which mostly reflects different routes of drug discovery. To take two contrasting examples:
1. A target and potential molecule are discovered and developed in an academic lab, following which a small lean biotech is 'spun out' to develop the molecule further. This biotech accesses funding, and spends an amount of money --usually in the low hundred-millions, but sometimes less-- running the studies and collecting the data necessary to approach approval. With luck and a following wind, they succeed, and their overall cost is low for the industry. (See the lower end of the table in [1]). If they fail, the biotech sinks without a trace.
2. A large pharmaceutical company need to continue developing new drugs to maintain its existence. It has a drug discovery operation or two, trying to find new targets and develop new drugs for them. There's significant attrition of these molecules here. Any promising molecules are taken into early-phase trials, where further significant attrition of these molecules takes place. Finally, if those studies are successful, the molecule heads to expensive phase III trials. Here, it's worth noting that the big players in pharma will have a combined R&D budget (encompassing all that we've mentioned here, plus some more) of multiple billions per year.
So for small single-molecule biotechs... Firstly the low end of the estimated development cost range ignores a lot of the discovery costs as they were borne by the academic lab. Secondly, the low estimates don't account for failure - as failed biotechs wouldn't be included in the estimates.
In contrast, the estimates for big Pharma do include their discovery costs, and can (in a decent analysis) also include the huge cost of multiple drug failures along the way to getting one drug approved.
Have a look at the linked analysis [1]. Rather than trying to estimate the cost of a single drug, it looks at the overall money spent on R&D versus new drug approvals in that time. (The methodology isn't perfect; but overall, it's probably a better picture of the cost of drug development across the board than a single-molecule estimate.)
[1] https://www.forbes.com/sites/matthewherper/2013/08/11/the-co...