In my use case, I was actually trying to stream a large gzip file from the cloud directly into subprocess without spilling onto disk or RAM i.e. the code actually  looked something more like:

r, w = os.pipe()
# ... launch a thread to feed r
with gzip.open(os.fdopen(w, 'rb')) as gz:
    res = subprocess.run("myexe", stdin=gz, capture_output=True)
## fyi, expected output is tiny
 
(In my case, I could modify the executable to expect compressed input, so I chose that solution.  Another possibility would have been to use subprocess.POpen twice, once with  'gzcat' and second with 'myexe')

I agree that given how libgz works, it would be difficult to fix the  problem.  I would suggest finding a way to alert the user about this issue because it will in general be a very confusing situation when this happens.