Yes, there is a big difference between the Main Outputs and the Line Outputs - but not sonically if the preamp is up to spec.
Main Output jacks, L/C/R: These are the ones you'll normally want to connect to when using most power amps. The output levels of these jacks are controlled by the Volume Control on the front panel and by the Trim controls on top of the preamp. The Center output jack is just a sum of the L/R channels.
Line Output jack, L/R: These are driven by the internal headphone amplifier, which also presents it signal at the Headphone jack on the front of the preamp. What makes this headphone amp unique is that it is a ~2.5wpc Single Ended Power amp built into the C28! This means you can hook up a set of very high efficiency speakers directly to the Line Output jacks and expect to get some decent sound out of it. When you read the Owner's Manual, however, you will learn that Mac recommends the use of the Line Outputs when driving long runs of cable to a power amp located elsewhere in the room. Also note that the Line Outputs have Trim controls on the top of the preamp that are called, Headphone Level.
Lastly, these two Output paths are driven by separate power supplies inside the C28. This means that you can have used the standard Main Outputs for years and never know that there might be a problem with the other Headphone/Line Output path unless you tried to use the headphones!
See the block diagram that's on the top of the preamp to follow the above description.
Cheers,
David