Dearest Umberto, just giving a quick update on the situation and all is working now and of course was something on my end not having anything to do with GSX. Somehow the Simulator itself wasn't reading the atc_id entry from the Aircraft.cfg for that particular repaint (all other variations using that texture and registration were working fine, just that particular one was not. Couldn't find why, but after removing that repaint and adding it back corrected the issue.
What a fantastic job you did regarding the option for specific aircraft/registration configuration! Very useful indeed!