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I am not sure time.strftime("%") should raise an error. There is an explicit test case and it's mentioned as platform dependent in the comment to raise a ValueError or succeed. So I don't know if it should be changed despite the inconsistency and there is any reason behind this.
The error regarding datetime module comes from SVN version and I couldn't get to know the original reason behind it and why the same was not carried over to time module. 
I agree with Eric that raising a DeprecationWarning for this and then removing it in later versions if we are going forward with this since we are making a platform dependent error as an expected error across platforms.
In the below test case "%" doesn't raise ValueError on my Mac OS and Ubuntu machine.
https://github.com/python/cpython/blob/9e95eb0d609cee23e6c9915c0bef243585b8c14b/Lib/test/test_time.py#L240
def test_strftime_format_check(self):
 # Test that strftime does not crash on invalid format strings
 # that may trigger a buffer overread. When not triggered,
 # strftime may succeed or raise ValueError depending on
 # the platform.
 for x in [ '', 'A', '%A', '%AA' ]:
 for y in range(0x0, 0x10):
 for z in [ '%', 'A%', 'AA%', '%A%', 'A%A%', '%#' ]:
 try:
 time.strftime(x * y + z)
 except ValueError:
 pass
I am adding @belopolsky who might have thoughts on the change.
Thanks for the report.