Will php documentation conflict with wordpress documentation?

I believe the practice of including additional data within PHP code comments is typically called annotations.

WordPress core makes no use of annotations technique for any code runtime tasks and doesn’t have an API for such purpose.

In number of context it will read file headers to extract meta data, such as main plugin files and some theme templates. As long as you follow documentation and include necessary elements for those I doubt you are going to have any trouble with them.