What part of this changes when a company is paying for the research, and why can't that same part be used in a government office? It's not like drug company CEOs and CFOs are also world class medical researchers. And if the funding decisions are entirely done by a CTO who is, then why would this model not be possible in a government office?
Ultimately someone needs to pay for all of the trials that don't work, and someone needs to do a cost/benefit/likelihood analysis on any research to decide whether it will be funded or not. With a public funding scheme, the benefit analysis could be based on public health interests. With a private company funding scheme, it has to be based on profitability. In healthcare, there is usually a huge gap between these two, unlike other more traditional markets.