I use WP Multisite already with subdirectories but I'm still in the "testing phase" of my Cloudron usage. I recently found out that at the Cloudron level, you can't add more than one top level domain, making one of the most important aspects of WP Multisite broken. It actually may be the only aspect of multisite that's broken on Cloudron (everything else works perfectly with subdirectories). This is, in fact, a Cloudron limitation and shouldn't be too hard to allow for domain aliases instead of only domain redirections (which breaks the built in WP Multisite domain mapping support). I've found a few users on this forum that want this. And, for me, to switch Cloudron to production, is a feature I'd need.
I'm getting more and more familiar with the Cloudron API, so I'll create a Wordpress plugin that when a domain gets mapped within Wordpress, it automatically adds that domain to Cloudron's domain aliases (if you decide to add this in addition to your current domain redirections) so that the experience will be absolutely seamless for users. I don't need this since I only run three mapped domains, but I want to make Cloudron the best it can be for the average user (the more successful you guys are, the more you'll be able to work on this platform that I'm growing to love). I've already made a plugin that does this very thing for CPanel so it won't be difficult for me to do so for Cloudron as well. I want to take as much load off the developers as possible so they can work on bigger picture Cloudron infrastructure (example: 6.0 stuff).