Yes, you're right, a computer has no "eyes" to see what's "up" or "down", although I don't know if the inner data structures of hexagon order the vertices in a consistent way that would allow to "classify" the vertices and make a coherent quad to triangles decomposition.
To reply that question we should be able to take a look at the source code of Hexagon (but Hexagon is not open source...so....) hehehehe...
A developer of hexagon could give a good answer. Sure!.
I've seen programs that have options to "flip" the triangle decomposition of quads too, perhaps that's an option for future Hexagon's versions (if any).
Non-coherent quad to triangle decomposition is good in some cases,
when you want to get nicer images under certain conditions.
See the book "Real Time Rendering" pages 269-274, 1st Edition by Tomas Moller and Eric Haines . ISBN 1-56881-101-2 , published by AK Peters.
Coherent quad to triangle decompositions is good in other like storing the
information in a compact way to render it extremly fast.