while not ideal, you can set breakpoints this way as well at the start of your main script:
and so on.
There is probably a way using objc to query all open editor files for breakpoints. An almost worked through way this would work: cycle through editor tabs
getting the filepath from .filePath()
checking for .editorView(), then
lines=[1+i for i,entry in enumerate(list(bps)) if entry['active'] ]
then add breakpoints as described above. This must happen after script is run, so either we pack this code into a import filebreaks, or else we can hijack pythonista_preflight the way dgelessus does in his pythonista_startup to disable global clearing.