Tough one...
As I see it, both have similar applications.
The Distortion is thicker and as such, may be better suited than the Custom in a 'dead' guitar. It'd make it more alive.
If the guitar is great already, the Custom may simply keep a little subtelty and 'vintage' vibe compared to the Distortion.
To my ears though, the Distortion is very musical and not even that much more modern than the Custom.
If you need this little more power, the Distortion is for you.
Otherwise the Custom maybe has a little more character but is a wee bit thinner.
They're hard to compare without having a proper sound in mind.