Thank you for the sample project. In the sample, you are setting DockSiteLayoutSerializer.SerializationBehavior = DockSiteSerializationBehavior.All, which effectively clears the MDI area's layout. The CanKeepExistingDocumentWindowsOpen option will ensure the documents that were open prior to layout load do remain open after layout load, but they have to fit within the new MDI area. Since you marked the document windows themselves to not serialize, and no other document windows have layout information serialized, no tabbed MDI containers are created during layout load. The non-serialized document windows end up opening in a new default tabbed MDI container following the layout load since the tabbed MDI host is empty at the time they reopen.
If you change the setting to DockSiteSerializationBehavior.ToolWindowsOnly, then it works how you want since that setting will not alter the MDI area.