Hi Andrew,
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I'd suggest not targeting a theme for version 4.9, since that is not only an older phpMyAdmin version, but the way themes are built is different. Starting with phpMyAdmin 5.0, we compile themes using SCSS files and some other major differences that don't give a clean upgrade path from version 4.9 themes to version 5.0.
To answer your question, I don't see a problem with you adding more directives in the layout.inc.php file; it's meant to be extended so I believe this is appropriate here.
Thanks,
Isaac