So rowCount() must return the correct value afterwards but can't be used internally.
Granted. But when is the table itself actually redrawn? During or after all the internal reorganization has been completed? Since many implementations of data() might make use of rowCount() to check the validity of the QModelIndex passed as argument and since data() is almost certainly called during the repainting, rowCount() would have to be valid at that point.

My hunch is that because the OP is using a single tree-shaped model to supply different information to different views, both views are reacting to the same begin/end signals. And as you mentioned, the row indices are probably correct only for one of the two views.