The thing is, the load of the workbee isn't outsize for transporters. That is, it could easily be beamed aboard container by container, by using one of those standard six-pad things.
Beaming eight containers aboard would probably also be quicker than towing that eight-container "train" all the way from the nearby space station. Not to mention that the transporter could take those containers to and from a planetary surface, while the workbee doesn't look at all like it could handle planetary takeoff and landing, atmospheric flight etc.
Then again, Khan's hut in ST2 appears to consist of exactly this sort of a container train - the mounting beam is still in place, and even has the clamps for a workbee at one end (although the bee itself is missing). Moving this cluster down would not have been possible with a six-pad transporter. But moving it down by a workbee doesn't seem plausible, either...
There are cargo transporters near the cargo bay. But moving from a StarBase to the ship would probably be more energy efficient by Workbee. While moving from ship to planet or vice versa would, the cargo transporter is probably more efficient.