Battery charge remaining of a brand new MacBook Air Retina doesn't match with Full Charge Capacity

This can be normal if the charging stops prematurely and can just be the difference in temperature or use at the time. As long as the Full Charge Capacity is the same you should be Ok. Do an SMC reset if you want. If you have any doubts run the Apple Diagnostic or take it to an Apple Store to be checked out.

I've seen it fluctuate in small amounts, but I have never really paid attention to new batteries. It wouldn't surprise me to see small differences since it is based on chemical reactions within the battery which can vary with temperature. You have at least a one year warranty on the laptop so I personally wouldn't be concerned unless you see a more drastic reduction.

The Apple battery status is usually fairly accurate and is a good indicator on the health of the battery. You can quickly check the battery condition by Option clicking the battery icon in the menu bar. The Apple Diagnostic can also sometimes catch a failure which may not be indicated in the status condition.