You could replace the commands to add the file to zip in the python script (see below) with your own python commands to create the file in the destination folder?
Replace these lines
zfAddNullFile(zf, f, (mtime.tm_year, mtime.tm_mon, mtime.tm_mday, mtime.tm_hour, mtime.tm_min, mtime.tm_sec))
zfAddNullFile(zf, dp, (mtime.tm_year, mtime.tm_mon, mtime.tm_mday, mtime.tm_hour, mtime.tm_min, mtime.tm_sec), 16)
with where you prepend your destination to both f & dp. e.g. f = target + f
open(f, "a").close()
os.mkdir(dp)
Though you would have to google on setting the timestamps accurately. see
here and
hereor use zerozipper by skwire and choose your temp directory to be the destination where you want the structure, but to prevent deletion you would have to ask skwire for the changes or the code