My understanding is that you should always have a spacer above your stem for a carbon fiber steerer. The issue (as I've read) is that if you put the top bolt of the stem too close to the edge of the CF, you may end up crimping the unsupported, open end of the steerer. With an alloy/steel steerer tube, you could always have your stem be 2-3mm above the top of the steerer and be fine.
But yes, in this case, flipping your stem is likely a better option for minute changes. I currently run with a 10mm spacer above my stem, and a 5mm spacer below my stem, which allows me to go 5mm up or 5mm down from my current position. I had 20mm extra sticking out before (for a total of 30mm above the stem), but that was definitely excessive.