Found the issue! Seems that the <Directory> in the .conf file in Apache2 was not configured correctly.
An example of a correctly configured .conf file is as follows:
# domain: exampleurl.com
# public: /var/www/html/exampleurl.com/public_html/
<Directory /var/www/html/exampleurl.com/public_html>
Require all granted
AllowOverride All
</Directory>
<VirtualHost *:80>
ServerAdmin [email protected]
ServerName exampleurl.com
ServerAlias www.exampleurl.com
DocumentRoot /var/www/html/exampleurl.com/public_html
ErrorLog /var/www/html/exampleurl.com/logs/error.log
CustomLog /var/www/html/exampleurl.com/logs/access.log combined
</VirtualHost>
Including AllowOverride All seems to fix the permalink issue.
Remember to run service apache2 reload in Terminal once you overwrite your .conf file.
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