IMHO, I think it is just a wording thing, even in the [?] popup on the profiler settings page, if you have a note to say 'includes framework methods', it would have been easier to find.
Having said that, it clearly tells you in the [?] prompt on the main window. I have never pressed the [?] buttons before, in fear that they open up a full help file that I have to wait for.
The other idea is that when viewing just in 'methods with source', the entry that appears on the tree :
*(Collapsed methods without source, such as framework class library methods)
:could have a note ! See 'All Methods' for deeper analysis of these calls.
Again, just thoughts.