As I mentioned in this thread, United now has implemented proper upgrade inventory for change-of-gauge flights with a single flight number. Agents were previously OK (even though it's previously been against the rules) with booking segments separately since the proper upgrade buckets sometimes weren't available (ie, NC on the domestic portion of an intl flight).

Since United resolved this issue, they explicitly instructed agents no longer to book change-of-gauge flights as two segments. They're presumably doing this so they can manage the upgrade inventory by market, which was their intent all along I imagine.