writing to the underlying filesystem is conceptually the same as writing to /dev/hda1 while you have it mounted.
in both cases the filesystem on top doesn't know about the changes below it and can be (fatally) surprised when it finds them.
later messages in the thread indicate that the warning is (somewhat) intentially overstateing the risk of an oops (rather then going into many pages of quickly obsolete details of what will fail)
I suspect that you get away with it by the fact that you are doing read-only on the result.
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