The US has orphan and rare disease programs that give bonuses to companies for tackling rare issues but you're right that we currently have a hole in the system. I wish there were a non-profit drug foundation that could go after stuff like that but I'm not aware of one.

One nit though: A ton of research is funded by the government, including drug research. We just don't have a federal program that requires commercialization of research to pay a royalty back into the program. If we did it would be a nice virtuous cycle, assuming some research continued to lead to viable products over time. Some universities have such programs in place for obvious reasons.