1) Macro applications get expanded immediately when encountered (well, modulo some fine details of type inference that are irrelevant here). This means that when you write handler[T], handler will try to expand with T as a type parameter. This won't lead to anything good, hence the error. To make this work, you need to turn Message.parse into a macro itself.
2) This happens because ReactiveMongo macros are unhygienic. Specifically, https://github.com/ReactiveMongo/ReactiveMongo/blob/v0.10.0/macros/src/main/scala/macros.scala#L142 isn't going to work correctly in situations like yours, because it uses simple name of the class, not a fully qualified name. I think the best way to make the macro work correctly would be using Ident(companion), not Ident(companion.name) - that would ensure that this identifier binds to the companion, not to something in scope having the same name.