There are four "styles" of service in Axis.
RPC services use the SOAP RPC conventions, and also the SOAP "section 5" encoding.
Document services do not use any encoding (so in particular, you won't see multiref object serialization or SOAP-style arrays on the wire) but DO still do XML<-Java databinding.
Wrapped services are just like document services, except that rather than binding the entire SOAP body into one big structure, they "unwrap" it into individual parameters.
Message services receive and return arbitrary XML in the SOAP Envelope without any type mapping / data binding. If you want to work with the raw XML of the incoming and outgoing SOAP Envelopes, write a message service.
So, if I use anything else except the first option(SOAP RPC Section 5), how does this impact interoperability? If someone says they want a SOAP service (including WSDL), does this mean that SOAP RPC conventions are expected? Can the other three styles still be used when the other end is not implemented with Axis?