Exceprt form the online help: "The update actually happens twice during the build; once right after the check out, and once before the build is completed."

As a result, when setting the build alias, you cna end up with 2 aliases if the information you use, is not available on the first pass (or change before the second pass).
Normally I would think you only want the final version (that is my use case), and would like to see the plugin cleanup the first alias when it differs from the second one.
(maybe some other users would prefer to have a checkbox config item to be able to preserve both ?)