All of the train connections in our reservation system are entered manually by our national train operations center, after considering operational feasibility of publishing and guaranteeing the connection, on top of the simple "legality" under tariff rules. However, you are right that many otherwise workable connections are simply missing, or are available from one city but not from another.
The solution we have proposed to our agents is that if they feel a connection really should be available, but isn't, they can submit it to a supervisor for review and escalation if a customer asks for it. AGR can then ask train operations about adding it to the connection table; however, this is not an immediate process and research can take a few days. On the bright side, if a connection is added, it will be available to all other customers who might want it later, whether paying with money or with points.
For consistency's sake across all agents, the default will be to only book automatically generated itineraries. There is no other lowest common denominator that will ensure a consistent member experience, given the way our reservation system operates today.