depending on their implementation, it may be possible to do click-free changes of the dsp graph, which is the weakest part of the dsp engine of pd.

This recalls me of a possibly unrelated even "bigger" problem: you get audio dropouts even by opening a window (such as a subpatch or abstraction by right click -> open). Why? Is the dsp graph redrawn when opening a window? Is there a reason for doing that? Or is something else the cause for such dropouts (maybe some memory allocation)? But then, shouldn't _anything_ happening when opening a window affect _only_ the gui process?