I think that I've read the same bookI read a book about how to prepare for Monbusho research scholarship, and it stressed that point too; but I really can't understand how they expect someone who just got his bachelor to have significant research skills.
I don't know how it works in your country, but here in Italy you just study and take your exams. That's it (except maybe for the thesis, didn't get there yet).
However, according to my understanding, Monbukagakusho is not a gift given to students that had high grades in college. It's rather a research scholarship given to people that can conduct research which develops the sciences in Japan
Now, conducting a research on your own is not something done only by "exceptional geniuses". Conducting a research simply means examining the latest research in the world in a specific field and trying to enhance it.
For example: suppose that you are a Civil Engineer. You read somewhere that adding tree bark to concrete will increase the strength of the mixture. When you read the research carefully, you find that this happens because of the cellulose concentration in the bark. Now the next step that you can take is that you find a material in other research fields that can enhance the concrete more....
Although my statements above might sound confusing to some of the applicants, you should remember that the final selection depend on your ranking among candidates which means that you might get the scholarship even if you have little research background