This example should lift any doubt about what to measure; note that in the first two cases the hairlines are perfectly superimposed to each other, showing that there's no issue with \Shortstack.
On the other hand, the difference you measured is less than 0.4pt, too small to be really noticeable: it depends on the bounding boxes of the characters.
\documentclass{article}
\usepackage{color}
\usepackage{stackengine}
\newcommand{\hairline}[1][black]{%
\leavevmode\kern-0.05pt
\smash{\color{#1}\vrule height 20pt depth 20pt width 0.1pt}%
\kern-0.05pt
}
\begin{document}
\centering
\Shortstack[c]{\hairline{}XXXXXX\hairline{} XXXXXXXXXX}
\hairline{}XXXXXX\hairline{}\\ XXXXXXXXXX
\vspace{20pt}
\Shortstack[c]{%
\hairline[red]Cognicion\hairline[red]
\hairline[green]abstractiva\hairline[green]%
}
\end{document}

\frameequivalent tofbox? – NVaughan May 25 '16 at 14:46\frameis more or less\fboxwith\fboxsepset to 0pt but it's from picture mode so the line thickness depends on \thinlines, \thicklines rather than \fboxrule – David Carlisle May 25 '16 at 14:52