Consider this snippet:

from doctest import OutputChecker, ELLIPSIS
print OutputChecker().check_output('AAA....',
'AAA.BBB', ELLIPSIS)

I expect that to print True, but instead it prints False.

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Sorry, but this won't change.  As in most simple parsers, a
"maximal munch" rule is at work for recognizing
multi-character tokens:  your pattern gets parsed as

    "AAA" <ellipsis> "."

not as

    "AAA." <ellipsis>

or as

    "AAA...."

Therefore it matches all and only those strings that begin
with "AAA" and end with ".".

The maximal-munch rules gives an easy-to-predict way of
resolving ambiguous inputs, but you're stuck with the way it
 picks.  Because of this, there is no direct way to use
ELLIPSIS to get the effect I'm guessing you want (i.e., I'm
guessing you want it parsed as

    "AAA." <ellipsis>

).