I agree that the warranty makes the difference and is well worth it for enterprise operations. I have not seen the problems you describe here with any systems I have built. Most people opt to make custom PCs either because it costs less money or they can't get the exact configuration they want from the big boys. That being said I once overheard a past employer say "If I had an Admin that wanted to sit around all day and build all my computers by hand I would fire him". There is a time and a place for everything. When you have a client that owns a small business that needs a custom, purpose built solution and wants to get a good deal on it I see no problem with making something just for them. It should be made clear that there is no warranty beyond what you can offer yourself. Do you want to be supporting these systems or would you rather have DELL do it? Maybe you are the DELL certified repairman for this area and you would do the maintenence yourself anyway. I'll bet if you were, you would rather install a system that you built yourself! (You would know better ;-D)

So I conclude that different things are good for different situations. There is a time and a place for everything and there is no one size fits all solution. If you make rules that you should always do things one way you not only assert that you have thought of everything that could ever possibly happen but you also limit yourself to the decision you made.