This stuff should be sorted out in Pd-extended as of 0.40.3. Pd-vanilla incorporated some of that code in 0.41, but not enough to fix the whole problem.
A sketch of the GUI differences a cross the different platforms.
On Mac OS X the Command keys is used instead of the Ctrl key on Linux and Windows.
Clicking a subpatch objectbox on Mac OS X brings the subpatch to the front even if it's already opened. This doesn't happen on some Linux window manager configurations.
On Mac OS X dragging the icon of a Pd file to the Pd application opens it. If an instance of Pd is already running it will open in that instance. In Linux, drag and drop does not work and opening a patch outside of the pd window opens the patch in a new instance of pd.