I am developing in a namespaced DE org (not packaged yet) and using standard SFDC_DevConsole debug levels (Apex = Debug, System = Debug, DB = Info) with no trace overrides. But all I see in the logs are my debug statements, queries, profiling info, and rows showing ENTERING_MANAGED_PKG.
This is a relatively newer org (created in late Feb 2016) and I haven't seen this behaviour in other managed DE orgs. So I can't tell where the problem is.
Btw I'm not sure if others have noticed this but the debugger has become somewhat unreliable as of late. For instance overriding debug levels for Apex classes does not always kick into effect. This was experienced recently in a customer org.