The difference is subtle and I am not even sure all native speakers would make the distinction.

In the first sentence, the indicative is sufficient since you do not express the hypothesis that he did or did not go: it merely underlines that the evidences brought forward prove nothing.

On the contrary, what is expressed in the second sentence is the heart of the problem which immediately brings you to the underlying question: whether he made the trip or not. Hypothesis meaning subjunctive tenses, the verb must be “n’ait”.

“Celles qui sont avancées” (those brought forward) refers to the proofs of the first sentence (the “absolute proof that he did not make the trip”); “celles” — those proofs — are evidences that must have been referred to earlier on. “n’en sont pas” means that they are supposed to be proofs but they do not stand up under examination of the facts and emerge as mistakes.

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).

The subjunctive is used to express the uncertainty of a fact or the wish or just possibility that it were so (or otherwise).
So, “Il y a une preuve absolue que Marco Polo n’a pas effectué son voyage” does not call for the subjunctive as an absolute proof makes a certainty. And, even if negated, a certainty remains a certainty. A proof may exist or not, but in both cases it is a proof that he has and not that he would have. (“il dit que un plus deux font trois”; “il ne dit pas que un plus deux font trois” changes nothing to arithmetic)
The hitch is that this reasoning applies exactly the same way to the second sentence too!
I think you have noticed it 😉
It sounds to me that the error is more in “preuve absolue” than in the subjunctive.
Why the heck would we need more than one single absolute proof? Worse, how could there be more absolute proofs that he did than absolute proofs that he did not? I think you got that too 😉
So, put it “pas beaucoup [plus?] d’indices que Marco Polo ait bien réalisé son voyage” and it becomes half right. But it means that that MP is said or supposed to not have traveled.
It sounds too that he rather means “pas plus beaucoup d’indices …” but let’s stop here 😉
BTW, many advices regarding subjunctive are recipes saying that some words call for it.
That is deceiving, as it may be used or not with those same words depending on the meaning.
It’s better to “feel” my first sentence and rely on that, although it can be a tiny bit more subtle. The subjunctive is needed only if those words mean what I say.

“comment se fait-il qu’il pleuve?” is wondering about the weather forecast.

“comment se fait-il qu’il pleut?” is wondering about vapor condensation.