Having multiple bootstrap files for apps removes the possibility to maintain the order of the nodes in the repository. In the Pages app the module version handler has to fix the order at install time. This should be removed.

As a general guideline have one xml file per "entity". The entity is a contentNode node sitting down a number of folders. The folders and the entity node names go into the name of the bootstrap file, the entity itself and all its sub nodes goes into the file.