Feeding in enclosure is the way to go. I've never had luck with feeding in a seperate enclosure. Generally when someone refers to feeding in a seperate enclosure, they are talking about a very temporary enclosure with no bedding that the snake is in solely for the purpose of eating. They are then transported back to their normal enclosure.

Pros:
-can't ingest any substrate
-sometime picky eaters will eat in a new, clean environment.

Cons:
-changing enclosures can stress a snake out; therfore it won't eat.
-snake smells food already when you move it to/from enclosure, increases chance of being bitten.
-you can leave a f/t food item in for extended periods of time without worrying about potential snake escape or wrong temps/humidity

I also find that snakes in their own enclosure are already in a comfortable and relaxed position, ready to eat whenever. However, when you move them, they need to get adjusted and in proper position for food. Just my experience.