Following up with this as this appears to be expected behavior according to another staff member:
Essentially what was happening was I would take all the descendants of the house, break their parents (parent to nil), and then rebuild in an order to load it in. On the load in, even though it would load back into an atomic model, it would do it in batches and may not send the entire atomic model at once. This breaks the atomic snapshot, thus resulting in an atomic model not being atomic
This should be documented somewhere. Developers expect atomic models, no matter how they are instantiated in, to actually be atomic