The likelihood is that it's a plot device, if for no other reason, to mix up the action with some flashy special effects.
But we don't like those answers here as Tron fans, now do we?
It's more pleasant to generate answers that jive with the story in ways less related to the unfeeling science of making films.
I think your theory about hard drive space is as good as any, IWB. I like it. I personally think Sark only has the carrier active when he's using it to monitor daily activities on the system. When he's reporting to the MCP in person, to leave the carrier running outside is probably a little disrespectful to the MCP, sort of giving him the impression Sark would rather be someplace else. I think it's just a respect thing turned protocol.