@marcusquinn I am late to this thread and have no experience with Wordpress Developer on Cloudron, just Wordpress on other platforms, so my suggestions here might be irrelevant...
(1) WP CLI has a plugin deactivate command: wp plugin deactivate <name of plugin> which perhaps can be added to a regularly scheduled cron job to allow Fluent SMTP to prevail. When a Cloudron update happens and SMTP Mailer becomes active, the cron job would deactivate it again. You can also delete plugins via WP CLI. This is not an elegant approach, just a hack that might work. Also, WP CLI can be run remotely via SSH, so if that is preferable in your environment, that can be done as well.
(2) A native Wordpress solution might be to use a plugin like WP Crontrol where you could add an event to deactivate SMTP Mailer. I don't know if there is a plugin deactivate event or if you could run a WP-CLI command as an event.
(3) Another option is a pure PHP solution driven by cron where the script would check for the existence of the SMTP Mailer plugin folder, and if found, delete it. (Note: Never tried this before, so be careful!)
Hope one of these is possible, and if not, perhaps it triggers some other ideas!