I presume that PyUnicode_FromFormat is responsible for the first of the following:
>>> '%010.5d' % 100
'0000000100'
>>> b'%010.5d' % 100
b'0000000100'

I am strongly of the opinion that the behavior should be left alone and the C-API doc changed by either 1) replacing 'exactly' with 'nearly' or 2) adding the following: "except that a 0 conversion flag is not ignored when a precision is given for d, i, o, u, x and X conversion types" (and other exceptions as discovered).

I took the terms 'conversion flag' and 'conversion type' from
https://docs.python.org/3/library/stdtypes.html#printf-style-string-formatting
https://docs.python.org/3/library/stdtypes.html#printf-style-bytes-formatting

I consider the Python behavior to be superior.  The '0' conversion flag, the '.' precision indicator, and the int conversion types are literal characters.  If one does not want the '0' conversion, one should omit it and not write it to be ignored.
>>> '%10.5d' % 100
'     00100'

And I consider the abolition of int 'precision', inr {} formatting even better.  
>>> '{:010.5d}'.format(100)
Traceback (most recent call last):
  File "<pyshell#2>", line 1, in <module>
    '{:010.5d}'.format(100)
ValueError: Precision not allowed in integer format specifier

It has always been a source of confusion, and there is hardly any real-world use case for a partial 0 fill.