Because certain genetic changes occur at a steady rate per generation, they provide an estimate of the time elapsed.
But, as Kumar and Hedges point out, Generation 4 methods have a number of advantages that will be useful for dealing with genomic data efficiently.
Specifically, they scale well with large numbers of characters or taxa, and they are free of the need for specification of clock models.
For example, as in any Bayesian analysis, choice of prior values (in this context, on node ages or speciation rate) in a dating analysis is complicated, controversial, and can have huge (YUGE? And while prior knowledge can now be modeled using a variety of age distributions and with the use of soft bounds, etc., friction persists at the basic interface of prior information (e.g., fossil ages) and prior specification.
These well-known issues have been spurring new methods aimed at more holistic incorporation of fossil and extant taxa into time tree generation.