Yes, I had lots of incidents in which replay results were different than real results. It seems like a kinda bug that will never get fixed.
Re. nailing your hypothetical army. It all depends. In this respect dominions is similar to chess. All the plans depend on timing, planning ahead and quick adaptation. So if your army where to be made only of Golems (so as not to lose SCs to charm) I'd have applied a certain method. Had your army consisted on only Rudra's a different method would have been used. A mixed force of them would have been the hardest to stop.
Delving into details is tedious, suffice to say that the ingredients to a response were at my possession. Or rather I was and still am under the impression that they were. Perhaps it was all wishful thinking
And yes, domes can indeed work against you as you have mentioned. Sometimes anticipation and stealthy troops/commanders can help with the reinforcements issue. I know this helped MA Man save the day in a number of sieges. Storming an otherwise empty fort that is in-fact protected by, say, 30 mothers and crones is all together a different story.