Indeed, this does create an issue. 

The last sentence in the documentation actually specifies where the encoding comment can be but doesn't strictly specify it can be on the second line if and only if preceded by `#!`.

I'm thinking the last sentence should contain the additional change, that is, change it from :

    The special encoding comment must be in the first or second line within the file.

to:

    The special encoding comment must be in the first line, or, if the first line is used to create an executable Python script, the second line within the file.

linking to (https://docs.python.org/3/tutorial/appendix.html#executable-python-scripts) accordingly. 

Let's see what Mariatta says about these proposals. Thanks for noticing.