The two examples above have identical markup, with one exception: the first example has "align-self:stretch" on the flex item, whereas the second example has "align-self:flex-end".
Currently, the flexbox spec says that main-size (height, in this case) is locked in (on the flex container & any flex items) *before* align-self is ever taken into consideration. So, the examples above should render with the same height, since they're identical aside from "align-self". (But Chrome and Opera/Presto render them with different heights.)
(Firefox versions 28 and higher match Chrome and Opera, per bug 903880.)