Looking through the logs that are currently present it seems that mysql/error.log and apache2/error.log are the only existing conflicts. Its possible to change the log name for apache2 for both the virtual host as you suggested @pb66 and the default error log in the sites-available emoncms.conf file, testing with the following works well:
<VirtualHost *:80>
ServerAdmin webmaster@localhost
DocumentRoot /var/www/emoncms
# Virtual Host specific error log
ErrorLog ${APACHE_LOG_DIR}/apache2-emoncms.log
# Access log disabled
# CustomLog ${APACHE_LOG_DIR}/emoncms-access.log combined
<Directory /var/www/emoncms>
Options FollowSymLinks
AllowOverride All
DirectoryIndex index.php
Order allow,deny
Allow from all
</Directory>
</VirtualHost>
# Default apache2 error log
ErrorLog ${APACHE_LOG_DIR}/apache2.log
I think this is a good solution that addresses the known conflict with minimal complication.
While there is a risk a user might install a package with a log that conflicts with another, the drop in logrotate config option still requires an awareness of this issue when new packages are added. Is it better to add the dropin logrotate overrides or rename the logs assuming that’s possible…?