The tree produced by TreeAnnotator (denoted the maximum clade credibility or MCC tree) is not a consensus tree such as that produced by the ‘sumt’ command in MrBayes. Instead, TreeAnnotator picks one of the trees actually present in the sample produced by BEAST – thus it is a tree that was actually visited by the MCMC sampler. The tree it picks is the one that has the highest product of all the clade credibilities (posterior probabilities) for all the clades in the tree. The motivation with this is to find a single ‘point estimate’ tree that is in some way central to the distribution of trees. This tree is then given (annotated with) summary information for the full set of trees from the sample. For example, it is given average node heights, credible intervals for the node heights, rates, etc.

See this page for various other approaches to summarizing trees.