In the last version of the Box Alignment specification both align-items and align-self initial value is 'auto'. This value should be resolved later to determine the computed value depending on the type of object.
For Grid and Flex elements 'auto' must be resolved to 'stretch'.
Since MathML renders implementation is based on the RenderFlexibleBox class, it's expected that 'auto' values are resolved to 'stretch' as well; however, since the nature of the element is based on the display property, some MathML renders have not these properties correctly resolved.
In the case of grid and flex containers, there is even an additional resolution logic at rendering phase, after the style cascade have resolved the css property values to their appropriated computed values. The case of MathML layout mode is particularly problematic because of the various render wrappers and their style handling logic it implements.
Fixed by http://trac.webkit.org/changeset/202934. MathML does not inherit from RenderFlexibleBox anymore nor does it use any align properties in its implementation.