I EPP and the way I work is put the hex's right sides together and whipstitch across the top with neat even stitches. I feel stitching "in the back" would be counterproductive and not hold well, also you could get some distortion. It is not uncommon to be able to see stitching from the front.
If you really hate the look of the stitching from the front, you can ladder stitch instead of whipstitching. Also if you work at a table and place the hex's face down and butted together then stitch, that prevents stitches showing from the front, but is a very slow way to proceed. Using similar colour thread to the particular fabric you are using also disguises stitching.
For my current project I am using the same thread colour throughout, but that is purely a personal thing and pertinent to the theme and design of the quilt.
You will never get a machine look from a handpieced item, that would be rather defeating the purpose. Even, neat stitches are the aim, and I am not advocating "sloppiness". If you can, take a close (zoom) in look at some pics. and you may be surprised at what you see.
Well, that's my take on it...and as a lone quilter am always keen to see what other quilters think.