Normally if you zip a .app directory on Windows and unzip it on Mac OS X, it won't run. This tool creates a zip file that should have the correct executable flags set to work correctly.

zip-app.py

#!/usr/bin/env python3
import os
import sys
import time
import zipfile

startingdir = os.getcwd()

if (len(sys.argv) == 1):
	print("Usage: " + os.path.basename(sys.argv[0]) + " path/to/application.app [path/to/output.zip]")
	sys.exit()

if (len(sys.argv) > 3):
	print("Wrong number of arguments - needs 1 or 2")
	sys.exit(1)

appdir = sys.argv[1]

if (appdir[-5:] == ".app/"):
	appdir = appdir[0:-1]

if (appdir[-4:] != ".app"):
	print("Error: " + appdir + " is not a .app file.")
	sys.exit(2)

dir = os.path.dirname(appdir)

if (not os.path.exists(appdir)):
	print("Error: " + appdir + " does not exist.")
	sys.exit(3)

os.chdir(dir)

appdir = os.path.basename(appdir)

zipname = appdir[0:-4] + ".zip"

if (len(sys.argv) == 3):
	zipname = sys.argv[2]
	zippath = os.path.join(startingdir, zipname)
else:
	zippath = zipname

searchname = os.path.join(appdir, "Contents", "MacOS")

zip = zipfile.ZipFile(zippath, 'w', zipfile.ZIP_DEFLATED)

for root, dirs, files in os.walk(appdir):
	for file in files:
		filename = os.path.join(root, file)
		
		if (filename[0:len(searchname)] == searchname):
			f = open(filename, 'rb')
			bytes = f.read()
			f.close()
			
			info = zipfile.ZipInfo(filename)
			info.date_time = time.localtime()
			info.create_system = 3; # Pretend file is from unix
			info.external_attr = 0o100755 << 16 # Set file permissions
			
			zip.writestr(info, bytes, zipfile.ZIP_DEFLATED)
		else:
			zip.write(filename)

zip.close()

print("Created " + zipname)

Thanks Draknek! I ported it to python3 and made an exe file here: https://gist.github.com/houkanshan/3c02a8f4487b2d343ae23522c9abe4f0

Could you tell me how to keep the soft connection when decompressing?

Updated to python3, and fixed some issues (previously it seemed to be working on Windows from WSL but not otherwise)