I don't think we should put too much effort into preserving numpy behavior.  Consider this python 3.5 session:

>>> import numpy
>>> a = numpy.array([1])
>>> bytes(a)
__main__:1: VisibleDeprecationWarning: converting an array with ndim > 0 to an index will result in an error in the future
b'\x00'
>>> a = numpy.array([2, 2])
>>> bytes(a)
b'\x02\x00\x00\x00\x02\x00\x00\x00'

It looks like this behavior is just an artifact of ndarray providing both __index__ and buffer protocol and not something thought out by numpy developers.

I wonder if we could check for buffer protocol support before detecting an integer argument?  I also recall a discussion of deprecating bytes(int) altogether.  See <https://mail.python.org/pipermail/python-ideas/2014-March/027295.html>.