Critical issues with the current canary might be what you’re thinking of, and I’m not sure if the unchecked repair checkbox means something got worse (compared to 2.0.3.3 beta) or that improvements aren’t set.
Release: 2.0.3.12 (canary) 2018-10-23 talks about a new Experimental – less potential for surprise than Canary which can drop major changes in too. Safest to read release notes, for example 2.0.3.6 warning.
On Linux, possibly Docker (which I don’t use) will let you have separate Duplicati “installations”, however keeping things separate is critical, because scrambling (e.g. sharing a destination) can create disasters.
Without that, keeping things separate might have to rely on a common base version with separate server folders (which you need anyway), allowing separate update channel settings and updates. Hazards exist. Basically you’re replacing risk from canary with risk from the setup and operation. Which do you want? 
On a positive note, having separate backup software to separate destinations is exactly what’s suggested when reliable backups are sought. One hopes that both backups won’t suffer a problem at the same time, however you’d be increasing the risk by having both backup products be Duplicati (though different ones).
can mean several things. such as reverting the structure (should be safe unless manual steps are wrong), reverting the content if canary breaks it (some people backup their database anyway for faster restoring if drive fails – use a secondary backup if you want this), but reverting destination files could also be needed.