Hello @Andrew
Many apps run their own NGINX or APACHE2 inside the app and can be configured on that level or on the application level.
For example Nextcloud has the /app/data/php.ini file where you can configure e.g post_max_size and upload_max_filesize to limit that.
Same for WordPress.
Ideally, each app should have the ability to configure this.
From your example, the apps ghost and peertube do not have a php.ini because they run NGINX inside the app.
Having the possibility to edit / configure NGINX directives there as well is understandable.
I will tag this topic as feature request to track this for the future.