I am trying to replace my stock SG Special pickups with new ones and have run into an issue with pole-spacing. The neck is 49mm and the bridge is 52ishmm, but I want to replace them both with standard spaced (49mm) humbuckers.
Is it possible to change the saddles on the TOM bridge to make all strings sit over their poles even if the bridge becomes 49mm?
or any other ideas?

No the TOM bridges arent gonna be adjustable there is a bridge available with adjustable rollers but it aint cheap. You could buy some blank saddles and file the slots with the new spacing. But that small difference in spacing shouldnt be an issue for the pickups.
it would be cheaper to just get an f-spaced pickup.
i used to be a mod, then i took an arrow in the knee.