Functionally they act the same but isnt a macrocannon just a scaled up bolter? Using explosive force to fire a projectile towards a target while Railguns use magnetic fields etc? Fluff question there, Imperial fleet stuff wasn't my speciality.
There is a difference between damaging and destroying though with regards to railguns. Railguns and Las cannons can destroy a titan by doing enough damage to them to force them to break down/collapse/blow up. Since they are capable of taking down some of the Imperiums biggest and baddest things out there, there is at least SOME chance, given the right conditions, which they can at least penetrate the ships hull. Never said it was a guaranteed but it's a risk. I mean don't get me wrong its not like either of them will properly cause any major damage to a ship beyond a few small breaches that cant be fixed, as you described, with a hand. The odds of damage would be minimal but I felt it worth mentioning. If anything though yes your biggest risk is collateral to hit anything else.
But we're getting sidetracked, I'd not ideally take them either unless you needed fire support for a long hallway and you're playing defensive and even then we're looking at last resort.