The spacing at your SG's bridge is probably around 52-53mm, as you say (depends how they notched the saddles at the factory).
But if you measure the actual spacing between the E strings directly above the bridge pickup, it's probably about 51mm.
The 50mm polepiece spacing is
centre-to-centre of the two outer poles, so strings spaced at 51mm should still fall well within the full "range" of the polepieces.
In other words, don't worry about it.

The only time this is really an issue is if you have a guitar with a Floyd or a vintage-style Fender bridge - then the spacing at the bridge can be as much as 56mm and you really can "lose" your E strings.