This may be too subjective, but here it goes:

PEP 8 discourages vertical alignment: "More than one space around an assignment (or other) operator to align it with another", but contrary to this rule, vertical alignment is used many times in the same paragraph, e.g.:
Yes: spam(1)
No:  spam (1)
If vertical alignment is so evil, the above should be changed to:
Yes: spam(1)
No: spam (1)

Disclosure: I use vertical alignment in my code quite often.

http://www.python.org/dev/peps/pep-0008/

Interesting observation :)  However, the alignment in the PEP is in prose, not code.

Correct, it is in mixed prose and code. However, the underlying principle in this PEP is: "guidelines provided here are intended to improve the readability of code". The author used vertical alignment (for mixed prose and code), because of its superior readability. Many others had found that aligning long columns of data improves readability, from newsprint and spreadsheets to multiple assignment statements.

This is a silly argument.

It's not *particularly* silly[1], but I think that with Government backing, he could make it very silly.

[1] I mean, the right hand side isn't silly at all and the left hand side merely does a forward aerial half turn every alternative assignment.

I admit, it is somewhat silly, but not entirely silly.