So, by Scientology's usual mandates, Tom should not be allowed to see Suri or Katie at all, as they have both split from the church. And yet, there's that whole "significant contact" thing.
It's no surprise, really, that Tom Cruise is above the laws of the Church of Scientology. After all, he's one of the highest-ranking members of the organization, so not only is he likely to have special privileges, but the church will also want to ensure that his prominent public image doesn't do anything to damage them. If Tom stopped seeing Suri altogether, the public would probably notice, and the church's harsh rules would be truly brought to light.