True, it seems to be the "Wappler" way of deploying stuff. That being said, it's worth mentioning Docker-Machine is deprecated, so it'll be up to Wappler to fix stuff if it breaks.
Right, you get root access with VPS servers, which includes DigitalOcean and Hetzner.
Right, as a system administrator you're responsible for applying security updates and such. You could also configure the server to regularly apply updates by itself (unattended updates).
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Getting started is easy, but either people use a managed database solution (like DigitalOcean's Managed Database) or they'll lose their data when the VPS fails and realize they don't have backups. The benefit of shared hosting is someone else is taking care of that for you (despite you should always keep your own backups).
Definitely, Docker would make things easier in that sense - everything would be setup exactly as the Wappler team wants.
But, if your website is famous enough and you get hit with a DDoS attack, you're effectively the SysAdmin, responsible for mitigating the attack at HTTP/HTTPS level. The same can also be said if the VPS crashes due to a hardware fault and you have to recover a broken database - Docker-Machine by itself will not save you as it does not know how to recover a broken database, it only knows how to run it.
When using shared hosting, recovering a broken database is someone else's job - even if it just means recovering from a backup of the previous day.
Docker-Machine seems a good solution for regular Wappler users due to being officially supported by Wappler (despite no longer being supported by the Docker team), just be aware of the limitations when stuff breaks to hardware failure and other catastrophes.
I personally use Caprover as I don't want to get tied to Docker-Machine (due to its future uncertainty), but you still have the role of SysAdmin in case stuff breaks.
Overall I think it's ok to use Docker-Machine, due to first-hand Wappler support.