The prefinished wear layers are much thinner, custom finishes end up about the same thickness in total. The main difference would be the custom finished take a bit of time to cure, ~ a week for water based and up to a month for oil. During that time they are more likely to mark, however the cure percentage is much higher the first days and tapers gradually from there.
For me as a contractor you can not beat the appearance of a well done custom floor. I've put them in my houses every time.

Sorry I forgot to answer your primary question.
Engineered floors are much more stable as moisture levels fluctuate. The newer sawn veneer floors are vastly superior to the rotary cut veneer products and worth every penny in price difference.

Unless things have changed in the last few yrs factory finished floors tend to have a higher resistance to abrasive wear than site finished floors. Aluminum Oxide can be applied at the factory under controlled conditions where site finished floors can't. The 'wearable' portion of the wood can sometimes be as much on an engineered floor than with solid hardwood. Lots has to do with 'design', stain and other factors. Some people just hate the beveled edges and other love them. Some houses with slabs or other conditions don't lend themselves to solid hardwood so engineered is the only choice