Yes they read
; Examples:
base_url[index] = http://aro.koyauniversity.org
base_url[aro] = http://aro.koyauniversity.org
; base_url[myOtherJournal] = http://aro.koyauniversity.org
htaccess reads
RewriteEngine on
RewriteCond %{DOCUMENT_ROOT}%{REQUEST_URI} !-d
RewriteCond %{DOCUMENT_ROOT}%{REQUEST_URI} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^/index/(.*)$ /index.php/index/$1 [L]
RewriteCond %{DOCUMENT_ROOT}%{REQUEST_URI} !-d
RewriteCond %{DOCUMENT_ROOT}%{REQUEST_URI} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^(.*)$ /index.php/aro/$1 [L]
and I have done this redirection to the short URL for OJS to work
RewriteEngine On
RewriteCond %{HTTP_HOST} ^aro.koyauniversity.org$
RewriteRule ^$ http://aro.koyauniversity.org/index [L,R=301]
Please note if I do it any other way the user page will not be found, as it keeps landing to http://aro.koyauniversity.org/index/user instead of http://aro.koyauniversity.org/user
Please see my notes of 16th June here