What do you think is missing in mastering a specific usage, say Matrix ? It seems to me FreedomBox installs and configures a specific package, let's say synapse, along with the needed databases; what more can it do ?
internetcube uses yunohost, so the quality of the box depends much more on a project that isn't tied to this specific box and can leverage improvements made by other users. yunohost is used for people who want to self-host with a machine they already have, or with a VPS.