Yes 409 rods are shorter than 348 rods but in my opinion if you are building a motor and care about your investment I wouldn't use them. They are one of the weak links in the ol motors, buying good rods is cheap insurance. Save them for wall hangers!
On a stock stroke,cast piston,,low rpm[under 6,000],cruiser engine there's nothing wrong with the stock rod.Build it for high performance,over 6,000 rpm, even occasional drags strip operation, no way.
I have taken the 409 rod with the factory 409/409 piston to 6200 regularly and to 7200 rpm a time or two.
Not to say I would recommended it, these had ARP bolts and was a balanced assembly.