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.
Best Answer
My understanding is that it should be possible to avoid the
ENTERING_MANAGED_PKGlog entries by using an Apex Code logging level above INFO. I.e. WARN or ERROR.Generally this works. However, there have been cases reported where changing the log level doesn't filter it out as expected. Voting for Debug logging level that will prevent ENTERING_MANAGED_PKG appearing in the log may help here.
With regards to the Developer Console not always applying the selected log levels. I found an oddity that was introduced in Winter `16 - Salesforce Debug logs with the Winter '16 Developer Console. Basically, by default all users share the same DebugLevel configuration. So if one user makes changes it affects all the users who are using the default configuration.