1) RedBaron uses a procedural API that modifies state continuously as you call methods on the class, whereas Bowler allows you expressive a series of queries/transforms up front, and then execute those all at once on your entire codebase. This also allows Bowler to provide a fluent API, so that you can chain all method calls from each other.
2) RedBaron uses a custom AST implementation, which still lists "Python 3.7 support" on its roadmap. Building on "fissix" (a backport of lib2to3) means that Bowler had day one support for Python 3.7 syntax, and already supports the provisional Python 3.8 syntax. This means your refactoring tools will never prevent you from adopting new versions of Python as soon as they are released.