Reliability? It goes like this:
Badly modded bikes < stock bikes < well modded bikes.
The bad mods come either from using badly designed/manufactured parts, people that don't know how to install them, or that do not think about systems as a whole (e.g. if you change an exhaust you might need to adjust the intake of air and fueling to match).
OEM components generally tend to be well made and reliable, but the manufacturers do have to work with a limited budget, and they do have to comply with emissions, noise, safety, and other regulations, that we as individuals do not (at least partially). Therefore every single bike has weaknesses, and there is basically no component that cannot be improved if you have unlimited money to throw at it.
Well modded bikes do not only use premium components but they are also put together with previous knowledge and experience of the builder (or by copying somebody who has been there, done that). Not everything that sounds great on paper actually works out in the real world.
A good example would be Colebatches X-Challenge. After doing 3 or 4 Europe-Siberia trips, and changing out everything that doesn't work or could be improved, that thing is solid. It's completely obvious that any stock X-Challenge ridden on the same track at the same speed will bend it's wheels quicker and generally break more shit (both because of inferior rims and because his suspension is better tuned and is more plush yet doesn't bottom as quickly), the aluminum subframe would break before his steel one, he would be more likely to crash at night because his halogen light puts out 1/5 of the lumens vs. the dual 50W Bi-Xenons, etc.
The same thing is of course the case with any other bike, and most other parts. If you want to leave something stock because you don't want to spend the money, don't have the skills, or you are fine with functionality as is, fair enough. But don't tell me you are doing it because "stock is the most reliable".