subtheme preprocess functions inheritance
EDIT : solution (can't answer myself before 8hours after posting)

Ok for those who're interested in the why :

It's a "side effect" of Twitter Bootstrap theme specific loader (_bootstrap_theme(), bootstrap_include ...)

To respect the correct order of hook processing, we have to keep the same filename as the main theme where hook is located in. (directories tree could change)

In my case, bootstrap_preprocess_region() was located in \sites\all\themes\bootstrap\theme\system\region.vars.php, so to overwrite it the mytheme_preprocess_region() should not be in my subtheme template.php file (=> breaking order of processing)

It should live in \sites\my-site.com\themes\mytheme\(opional folder)\(optional folder 2)\region.vars.php

Not explicitly written in TBS documentation I think ...

I hope this could help someone one day ! (: