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See page 13 of the 9'-17' Boston Whaler Owners Manual
http://www.whalercentral.com/download...p?cat_id=5

It says that basically:
"On 17 foot models or Limited models equipped with optional stern decks, access to the rear floor sump drain is restricted. The drain plug on these models can be installed from outside the transom."

End quote from above.
All the other models should be placed inside so you can remove them while boating if necessary.
Example:
If you take a wave over the bow, there would be no way to remove the plug to let the water out if the plug was installed from the outside. (or very difficult and inconvenient to say the least)

So, according to Boston Whaler, Drain Plugs go on the inside when at all possible.