First, be sure you use the latest vehicle updates installers, from the GSX page.
You can adjust the door's heights (but be sure you are using the current vehicles, first) using the included airplane customization editor, and you can choose the type of ULD used too.
The 767 should use the DPE type, which is smaller and of course, the one depicted in GSX has the correct real-world sizes and are indicated in the GSX manual. Of course, we cannot vouch (or doing anything to control) the accuracy of the cargo bay door for every airplane model out there.
For example, the default 747 doors are too small, so the (correct) AKE GSX container will not fit, but they works just fine on the PMDG 747, which is clearly more accurate than the default one.