Part of the issue is that the system kicks out changes from nonstop to connection. The rules only prohibit the reverse. As for the valid routing, I've been told and have never had an issue changing routing to one that isn't published. Agents are supposed to use some discretion so no MQM MRs. However otherwise it's ok, and doesn't need to meet any fare rule routing, SDC rules override fare rules.

I frequently as I've noted change to LAX-JFK flights flying out of cities so I can meet up with coworkers on the flight.