Not only the point system should be transparent to all users, but it also have to be explained to them. If we look at stack exchange, it's a great force they have to motivate the community.
If the point system isn't understandable, users may get suspicious about the intentions carried by the Q&A site.
We* are going to implement a Q&A site for botany, so we will have a community with an important part of scientists.
At the first presentation of the Q&A site project, they have been some suspicions about the point system. For exemple it was pointed out as a selfish way of promotion (!) ...
So explenations and transparency are not only relevant but in fact a fundamental issue in our case.
* "we" is here meant as the Tela Botanica french speaking network of botanists.