FYI, I think there is another issue regarding use of the VS publish feature with mojoPortal. Some features like Poll, Survey, Site Office, WebStore are implemented as external projects. On post build event they copy their files to the correct places under Web but since they are not part of web project I don't think they will be deployed by the publish feature. Again, UnleashIt solves this problem best because it packages files based on their type not on whether they are included in the VS project. So if you are implementing custom features in external projects I think you will have trouble getting your files into the package using the VS publish feature.
For best results use UnleashIt, the benefits of being able to implement custom features in external projects far outweighs the benfits of the VS publish feature and using UnleashIt keeps all the easy advantage of packaging files without losing the easy integration of external projects.
Best,
Joe