My understanding is YunoHost makes absolutely no attempt to isolate apps from one another, it just helps you install stuff on a Linux box. Unfortunately that means a single flaw in a single app compromises your entire server.
It’s was designed predocker and is a pretty old school setup. I remember they had issues updating Debian because the new Debian had a new php version which caused issues for some apps.
Yes, Yunohost makes installs very easy. But if something isn't working right then you got extra layers to deal with. I don't know how Sandstorm deals with this, but Yunohost taking care of the install and upgrade procedures means that you are bound to the Yunohost integration's version of the software. For instance when installing Discourse via Yunohost this version lags behind significantly. And also Yunohost disables the Discourse upgrade process, while it offers a superior experience.