You can easily configure it as what you do for VHD/VFS.
To disable/enable Auto-Pause, find the configuration checkboxes from HLE/Misc panel in Config->Setting of rpcs3.
Would have a configuration window (with create the list, and enable/disable, being something similar to VFSManger and etc).
Move the code to Debug::AutoPause in AutoPause.cpp and AutoPause.h
It triggers currently in GameViewer, and would finally change to somewhere else.
Well and now it is all enabled (Function call + System call) by default.