I'm in the process of considering either a LT or base model. What is swaying me to the LT is how clean the bike looks with the luggage removed. My luggage would likely be installed 10-15 days/year.
There are several after-market rack systems which have a quick disconnect system, so you can have a clean looking bike when the bags are off. There may be a small bit still attached to the bike, but you won't have the "rack" look.
The factory boxes are excellent except for the shape. I have a few specific things I carry when I commute to work, which do not fit well at all in the factory boxes. The boxes are not rectangular, so a regular shoulder bag doesn't fit. My lunch bag doesn't fit, either.
If you have specific items you will need to put in the boxes, take them to the dealer and see if they fit.
The Givi top box nullifies that complaint. The factory top box is exactly the same as the Givi V47 unit except the factory box is a lot more expensive, comes with a matching key to your ignition, and has a trim plastic panel which matches your motorcycle color. The top box is big enough to carry things which don't fit the side cases.
My recommendation would be to either save money by getting aftermarket racks/boxes, or get the full Kawi package with all 3 boxes with matching color panels and keyed to your ignition.
Though I don't especially like the appearance of top boxes, the V47 is very useful and well built. You may find you end up with one anyhow.