I'm (sadly) not particularly familiar with C, though I have tried to trace the calls of TkClipCleanup. As @taleinat mentioned, it is called by the TkCloseDisplay, though, in turn, I believe this method is called by the DeleteWindowsExitProc method. The name "DeleteWindowsExitProc" is passed, in the Initialize method, to the TkCreateThreadExitHandler method (I assume method references work in a similar-enough way to Python?) along with the tsdPtr object.

I stopped tracing it at this point, and instead worked from the Python end. The Tkapp_New method calls the Tcl_CreateInterp method and I have three questions about this (each only applicable depending on the answer to the previous one):
1. Is the Tkapp_New method the correct one to be looking at for tcl/tk initialisation (I can't find where _tkinter.create is implemented)?
2. Is there a reason why the call is to tcl rather than tk?
3. Would changing this to tk cause the fix in tk to be applied?