Todos os quatro dos seus < Directory > as sub-rotinas são definidas com caminhos relativos. Caminhos de diretório devem sempre ser caminhos absolutos completos (ou caminhos absolutos com curingas).
Eles são NÃO interpretados como se fossem relativos ao DocumentRoot.
Tente:
<Directory /usr/share/phpmyadmin/>
...
</Directory>
<Directory /usr/share/phpmyadmin/setup>
...
</Directory>
<Directory /usr/share/phpmyadmin/libraries>
...
</Directory>
<Directory /usr/share/phpmyadmin/setup/lib>
...
</Directory>
Na documentação do Apache 2.2: (2.4 é o mesmo)
<Directory> and </Directory> are used to enclose a group of directives that will apply only to the named directory, sub-directories of that directory, and the files within the respective directories. Any directive that is allowed in a directory context may be used.
Directory-path is either the full path to a directory, or a wild-card string using Unix shell-style matching. In a wild-card string, ? matches any single character, and * matches any sequences of characters. You may also use [] character ranges.
None of the wildcards match a '/' character, so <Directory */public_html> will not match /home/user/public_html, but <Directory /home/*/public_html> will match.