That is, of course, by design. To me (I have been a professional Smalltalk for a while), GNU Smalltalk drops the essence of a traditional Smalltalk environment and while I was "hmm, interesting, maybe if I ever have a use for it I'll look at it", I never needed it. A Smalltalk IDE is an extremely powerful fool, and IMHO the most powerful tool we've invented so far. Having said that - I do think that Pharo and friends maybe should be more friendly to what I as a developer expect today from my tools: mostly keyboard-driven, no overlapping windows, etcetera.
I think there are two separate design issues. One is the architecture of the Smalltalk development environment in terms of displaying information about classes and objects and lists of related methods and the running system and so on. That's great and and powerful and entirely orthogonal to the WIMP interface and the particulars of the screen presentation.
