Excellent thread, and many good points made on both sides of the issue. Hey, if you use a dual-purpose bike mostly on the street and rarely venture off-road other than a few rides down a smooth gravel or dirt road then you'd probably be satisfied with them as delivered. IMO that's the way most buyers actually treat them and the manufacturers set them up accordingly.
If you're more demanding of off-road performance then you have to tinker with things like suspension and engine response more than the "average" buyer. It's pretty much the way most SUVs are rarely driven off-road except for a small select group of owners.
As others have said, there's no simple answer as to whether that tinkering affects reliability. Mostly depends on if you know what you're doing and use quality components.