The word set is commonly used in sports and other activities where getting into position is a key part of preparing.
Etymology online defines it as meaning ready or prepared, first recorded in 1844.
Similar usages are on your mark, get set, go. (A similar phrase is ready, steady, go, which might be just as apt for your boat, as a steady boat probably races better).
Here, set is to get everything into position at the mark. It's more that being at the mark. As "set" is called, the runner gets his feet and hands into position in the block. A swimmer assumes the optimum position to start a race from either the block or the wall.
On a sailboat, we set the sails (not the same as "set sail"), by adjusting them just right for the course and wind.
We set the table, we don't just throw the dishes helter-skelter across it. (If we did, even our mothers would tell us we didn't set the table.)
Early usage cited in Google Books:
1889 Brawn and Brain: Considered by Noted Athletes and Thinkers - Page 67
At the word "set" lean forward, which sets your whole weight on your left foot...
1827 The Prose Works of Sir Walter Scott: Woodstock. Memoirs of ... - Vol. 5, page 25
Speak little, if you can, and lay aside your big oaths and swaggering looks - set your hat even on your brows.
This predates the first recorded date of etymology online, but, taken in context, it clearly is instruction about how to position the hat and not just to wear a hat.
1799 THE NAVAL CHRONICLE FROM JULY TO DECEMBER - Page 262
The Emperor was particularly attentive to everything on board the lugger, visiting every part of her, and when the sailers were hoisting the sails, he insisted on helping for once to set the sails...
No doubt there earlier uses with similar meaning can be found, but I'm guessing your question is really about how the word set came to be used in rowing, so I'll stop here.
Related "Difference between “On your mark, get set, go” and “Ready, steady, go”