Bearing to stem distance is not important as long as it all fits - a lot of pro riders set theirs up really low.

The manufacturers of most forks that have carbon steerers, like yours, recommend that there is part of the steerer column under the whole clamp area of your stem, which means leaving enough room to put a spacer ABOVE the stem. I have the EC90SLX fork, and I believe they recommend having a 10mm spacer above the stem, but other manufacturers recommend just 5mm, I believe. The compression cap then goes on above this spacer.

Therefore, you should either see if you can get a shorter headset top cap (some of the conical shaped ones for integrated headsets can be switched for something shorter) so that you can move your stem down by at least 5mm, or if this is not possible then make sure that you use a torque wrench and don't overtighten the stem bolts, and periodically check that your steerer is not cracking under the stem clamp.

Some stems are designed differently to others, because some like the Bontrager Race X Lite (or RXL as it's now called) have both clamp bolts near the middle, whereas others have the bolts at the very top and bottom. I'm not sure whether this affects where the stem's clamping force is distributed, but it's something that I've often wondered about. Maybe you can use something like the RXL with less spacers above it than a stem of a different design? For instance, there is about 5mm difference between the height of the top bolt in these two stems: