The aspect of prototype software that the author was calling out was that it is throwaway software.
Putting that aside, prototype software is recombining existing technologies and concepts in well trodden domains, which is distinct from the genuinely novel scientific work the author was contrasting with. Software prototypes are not in the same league, as much as you may like it to be.
Don't you think novel scientific work recombines existing knowledge? Isn't the saying precisely of standing on the shoulders of giants?
That being said I didn't compare both, not sure why you brought that up. I specifically discussed about prototyping, quoting a specific sentence, not scientific research.