No no, it's not that bad if you try to figure out where the commas go:

Not only are most eccentric opinions that have been held not accepted, those that gain the benefit of the eccentric opinions on their way to being accepted, are not necessarily those that first hold them.

So to rewrite with fewer negations:

Most eccentric opinions are not ultimately accepted. And when those rare eccentric opinions get accepted, their original accepters don't benefit much; but instead, the credit or rewards are reaped by those who accept them later in the acceptance process.