Well, you could always manually install anything inside a subdirectory - Cloudways won’t stop you from doing that. But of course you wouldn’t have access to Cloudways’ management options for things installed this way.
If you choose to do so, then every action (backup/restore/migration/clonin) will include everything - that is, the main app, and the subdirectory apps. Same with configuration options. In this scenario, you really won’t be able to manage them separately.
In any case, why not use subdomains? I heard it’s good for SEO (as it counts as a different domain).
Also, you could always set up a redirect from example.com/blog to blog.example.com