Probado en Debian Testing con la fuente de repos; sacado de los comentarios de: https://gist.github.com/IgnoredAmbience/7c99b6cf9a8b73c9312a71d1209d9bbb; checkear cosas de fonttconfig que se mencionan ahi (todo que nunca hare jajaja)

99-color.emoji.conf

<?xml version="1.0"?>
<!DOCTYPE fontconfig SYSTEM "fonts.dtd">
<fontconfig>

    <match target="pattern">
        <test qual="any" name="family"><string>monospace</string></test>
        <edit name="family" mode="append" binding="weak"><string>Noto Color Emoji</string></edit>
    </match>
    <match target="pattern">
        <test qual="any" name="family"><string>serif</string></test>
        <edit name="family" mode="append" binding="strong"><string>Noto Color Emoji</string></edit>
    </match>
    <match target="pattern">
        <test qual="any" name="family"><string>sans-serif</string></test>
        <edit name="family" mode="append" binding="strong"><string>Noto Color Emoji</string></edit>
    </match>

</fontconfig>