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I suggest to everyone to follow what Boston Whaler suggests and prints in their documents.
Everyone please read page 10/11 of the Owners Manual for 9-17 models under Auxiliary Engines.

I can think of a couple of other reasons why you probably would not want the 25 inch shaft and there are probably more reasons then I can think of.

1. Will the motor tilt completely out of the water when underway without dragging? Some boat/motor combinations will not. Might create a big rooster tail for show though.

2. The extra 5 inch length gives more hanging out the back when even tilted up which can bounce much more on the transom possibly creating problems like cracking, breaking, the transom etc. when underway or when trailering if in the up position.

3. You are already talking about a 4 stroke which is heavier then a 2 stroke, plus now you are adding another 5 inches of shaft. How much more weight is that?
You don't mention what size and weight the main motor is.

The list could go on.

Good Luck and let us know how it works for you.