i think if you visited the american design thread youd get different opinions than that on this thread
Sort of. Lefties on that thread mostly love it since they can buy and design things that are actually not available.
In terms of true custom options, there are some, not a whole lot in factual practice though. I know I'd love to see bound necks available on more models.
Upside, you get your mods installed by Fender at the factory with a COA so resale will be untainted by those additions. Downside, it's often cheaper to buy stock and modify to those specs.
I'd also suggest you read the thread. I know a few folks have had issues with their orders; more than you'd expect based on the number of people involved with the thread.