Yeah because that's how the military operates, they just totally trust civilian organizations with top secret projects and don't keep their at least their top people informed. When Paul Tibbets took off in the Enola Gay the Army Air Corps just told him he was going to be doing a little experiment over Hiroshima that day.
Most military/corporate projects operate under a "need to know" basis. Your premise misses why does the Reliant need to know anything more than "find a lifeless planet"? The Genesis people would give the parameters they need for said planet. They would be under no obligation to share with Reliant why they need that type of planet. They would be under obligation to share with Starfleet Command the information because it is Starfleet that is allocating the resources for the project.
Now, if Reliant were to ever serve as the delivery system for the project, then we have a different matter. But its involvement would still be limited to the actual delivery and they still wouldn't have the nuts and bolts information needed by Khan to construct the device. Anymore than Kirk and Spock got the schematics to M-5 before it was installed aboard the Enterprise. Scott likely got limited information on how to hook the M-5 into the computer network.
People have their pet theories picked apart here every day (I know I have), so don't feel special.
