Redesigning default ships at game start?

Don't think you could say they were flawed, in so far as they work. Depending on starting techs there may be something you would want to add that isn't included on the stock model (sensors/life support/engine for example).
One of the main uses is the upgrades. You can upgrade a custom coloniser to a constructor and vice versa. Given the long transit times you generally have at the start of the game this can come in handy. For example, if the AI colonises a planet before you reach it, you can switch the coloniser to a constructor and go grab any nearby resources instead.

The core designs are the same for all races, so they don't take advantage of any additional techs you may start with. As applies to colony ships, this redesign usually means cramming more engines on them.