Why? This has to do with torsion and with "beating a fish" using the blank, i.e. using the entire leverage of the blank to fight a fish. The greatest leverage is against the strongest side of the blank.  Therefore, boat rod guides and reel seats should be aligned along the stiffest section of the rod. If they are placed not on the 90 or 180 degree (stiffest side) the rod will have a tendency to try to rotate away left or right of center.  On light tackle this is not noticeable in fighting a fish, but is quite noticeable in casting for distance or accuracy. 

The current on-going debate among rod builders revolves around fly rod blanks and whether the rod will be used for distance casting or for "soft presentations" on smaller chalk streams.  The jury is still out with rod builders trying to determine the efficacy of guide and reel seat placement on the stiffest side or 180 degrees off that.  The basic thought is that if the guides are configured like a spinning rod then the back cast will be longer and the ability of the angler to bring a fish in to the net will be faster.  The opposing camp feels that placement of the guides similar to a boat rod should produce a softer presentation, and might actually cast farther as well since the "load" on the blank is actually on the back cast.  

The jury is still out and testing these theories is difficult, because no two rod blanks are exactly the same so building comparative rods on the same blank might not be a good indication (one spline might be more pronounced).   Other builders have tried to place guides on both sides of the blank to test the same blank on opposite sides of the stiffest spline.  Of course this means that both sides will be "damped" by the additional weight and wind resistance of the second set of guides. Eventually this will be tested adequately - but constructing the test is difficult. 

In any case, when selecting a rod from an off-the-shelf situation you should check that the guides are at least placed on either the same side or the opposite side of the stiffest longitudinal surface of the blank.  Off-sets from that will cause disappointment as casting will be poorer (shooting left or right of center) and bringing a large fish (deep pelagic specimens) to the boat will be much more tiring, especially on the fisherman's forearms and wrists.