We used to package a WAR file in our distribution but no longer do so (although you may still find the WAR file online):

BSERV-2749 - Getting issue details... STATUS

Currently, when the Bitbucket Server distribution is built we simply unpack the .war file into the atlassian-bitbucket directory of the distribution however, this may not always be true. To this end we ask that users use the standalone distribution as we are likely to add functionality to Bitbucket Server outside of the main web application (e.g. Search as a separate service that we start when we start the Bitbucket Server application).