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I think the 408 is more popular because the stroke on a 427 is larger than the bore. a 408 is a 4.03" bore with a 4.00" stroke. Also there is more notching on the bottom of cylinders.
The real reason is that the more you stroke an engine the shorter its life because you add lateral forces to the piston with the wider rotation of crank and resulting angle of the rods. A 393 or 408 stroker will last much longer than 427 stroker. Race cars will go 427 because the engines are rebuilt fairly frequently anyhow, but if you want a car with an engine that lasts I wouldn't go more than 408.