These issues have been concerning me, as I am currently building up a new bike with an Edge 2.0 Road fork and a Thomson X2 stem, which has a cutout. The Thomson site specifically states that the stem is okay for use with carbon steerers. The Edge site does not say that a stem with a cutout will increase the chance of failure. I still plan on contacting Edge to make sure this combination is okay.
The Edge site recommends a spacer above the stem and installing the stem with a torque wrench. They are specific about the amount of torque that should be used in the installation. The Thomson site is very specific about where the steerer tube should be cut relative to the stem cutout and bolts.
Trek seems to think that the cutouts are enabling more sharp edges to dig into the tubes, causing the failures. I did notice that the Thomson stem seems to have a slight bevel around the cutout where it would contact the steerer tube. It would probably be wise, if a stem does not have this sort of relief, for a builder to relieve any area of the stem where it might contact the fork with a sharp edge; some very light work with a file or something.
Of course, any modification of any part would void that part's warranty whether or not the modification did any real damage to the performance of the part. In the case of relieving the edges, it might actually make the part safer. Its just a way for manufacturers to cover their asses. I also feel that it is easier for Trek to just blame the stem manufacturer, rather than own up to poor design on their part.
I plan on having my fork painted along with my new frame. Every carbon fork manufacturer says this will void their warranty. Plenty of carbon forks are painted with stock frames. The issue is that it is not done in-house. If it is done by a competent, experienced painter, a coat of paint should not cause catastrophic failure. But, since the part was "modified" by someone not in-house, that person must be the one responsible in the event of catastrophic failure.
Manufacturers are so focused on the lighter/stiffer/more compliant marketing strategy that they are blurring the lines on what is safe to ride. If you want to go lighter, and a part needs a rider weight limit, give it a rider weight limit. If its still iffy, don't put it in the marketplace. But if you do release a part and it fails, you better own up to it or hope the rider dies. Because consumers relay negative experiences 2 to 3 times more than positive ones.