Where in the 2005 code does it state that romex cannot directly feed the dishwasher(romex in wall wired directly to the dishwasher junction box)or is it just a protection issue and needs to be sleeved in flex from wall to dishwasher JB?

The NEC doesn't prohibit connecting directly with NM cable but the majority of the dishwashers I inspect are cord and cap connected for three good reasons.

1. It's easier to connect a cord before they install the dishwasher and have a receptacle in the sink base cabinet to plug it into. Cord to be 3-4 feet long max. See 422.16(B)(2)
2. You now have no issues with having a disconnect at the appliance.
3. The plumber now doesn't have to deal with a hard wired connection when he/she has to pull the unit out for servicing.

How do you resolve "closely follow building finish" and "secured ... within 300 mm (12 in.) of every cabinet, box, or fitting."?

That's reason number 4. to use a cord and cap ::