It is indeed a flaw, though it is in itself already a fix for the single-instance services, such as Reddit.
If an instance becomes unavailable/defederated on the fediverse, a large portion of content will become unavailable, but the service will still be functional. If a single-instance service becomes unavailable, or if the admins do something stupid, ALL data will be jeopardized.
I know that this might not be the answer you seek, but I think it helps adding perspective to the problem.