Carbon steerer with expander plug under the stem, should I be worried? I just bought a custom fixed gear frame that comes with a carbon fork with carbon steerer, off a guy who already cut the steerer lower than the stem so that the cap can sit flush on the stem. Normally I would put a 5mm spacer above the stem, because it seems like the general best practice.

However the fork was already cut so that with the expander in, after tightening the cap, the top of the expander plug would leave 2mm below the stem. I might be able to find a way to shave the top part of the headset a bit to save like 1mm, and since this frame hasn't been ridden, it should settle in just slightly deeper after a few rides.

Either way, should I be worried? or is this normal that it is not a problem?
Should you be worried, I wouldn't be. The alloy expander will stop the carbon steerer from being crushed. Remember the max torque on the stem bolts will likely be less than 6nm. (Use appropriate retaining paste and don't over tighten it!) 

As you mentioned, a lot of people (me included) will recommend a 5mm spacer on top of the stem, with the steerer a bit longer, to be extra safe. 

But plenty of people refuse to have spacers above the stem for various reasons, mainly aesthetics, and they are fine, assuming the expander insider the steerer is of good quality.