In this case the difference is to be sought in the author's point of view.
In French the subjunctive can be used, as it is the case here, to express a hypothesis, a light doubt, or to distantiate oneself from an expressed point of view or opinion. A stronger doubt can sometimes be expressed through the use of the "Conditionnel" (cf the German language with the Konjunktiv I used by Journalists, and the Konjunktiv II to doubt).
To use your example:
There is no proof that Marco Polo didn't make his journey.
No hypothesis, it is a clear statement. But in the following sentence (feel free to edit if you find a more correct way to express this in English):
There isn't much more proof, however, that Marco Polo "wouldn't have made" the journey.
Through the use of the subjunctive (which is here optional), the author makes clear that for him there can be some doubt as to whether Marco Polo did make the journey or not. Or at least, he presents it as a hypothesis (which is reinforced by the "bien", i.e., really in this context). It is a very subtle difference.
However, the author probably wrote in the subjunctive mood out of habit,
because it is often required in a complex sentence expressing an opinion, a hypothesis, a wish, a state of mind or an emotion (like in "je suis content que vous posiez cette question"). When the second part is in the subjunctive present tense, the only requirement for the first part of the phrase is that it has to use the indicative mood, present tense (fulfilled in your example).
It would have been perfectly correct to say:
Il n'existe pas beaucoup plus de preuves absolues que Marco Polo a bien réalisé son voyage.
To my eyes the last sentence is even more correct because the slight doubt is already meant in the sentence, so there is no need for the subjunctive (although it is grammatically correct).