This can be closed, but for completeness, the test you ran didn't verify that the bug was fixed. This is because the hard coded compile flags I gave in my example seem to have changed in Python 3.9 (is this documented?). 

In python3.8 the compile flags I specified correspond to division, print_function, unicode_literals, and absolute_import. 

python3.8 -c "import __future__; print(__future__.print_function.compiler_flag | __future__.division.compiler_flag | __future__.unicode_literals.compiler_flag | __future__.absolute_import.compiler_flag)"


Results in: 221184


In Python 3.9 the same code results in: 3538944


I can modify the MWE to accommodate these changes: 

./python -c "import __future__; print(eval(compile('[i for i in range(3)]', mode='eval', filename='fo', flags=__future__.print_function.compiler_flag | __future__.division.compiler_flag | __future__.unicode_literals.compiler_flag | __future__.absolute_import.compiler_flag)))"


Which does produce the correct output as expected. So, the issue can remain closed. I am curious what the bug in 3.9.0a5 was though if you have any speculations.