HADOOP-15051 as wontfix. LocalFS output streams don't declare their support for hflush/sync for the following reason, as covered in HADOOP-13327 (oustanding, reviews welcome)
Output streams which do not implement the flush/persitence semantics of hflush/hsync MUST NOT declare that their streams have that capability.
LocalFileSystem is a subclass of ChecksumFileSystem; ChecksumFileSystem output streams don't implement hflush/hsync, therefore it's the correct behaviour in the Hadoop code.
If HBase requires the methods for the correct persistence of its data, then it cannot safely use localFS as destination of its output. It's check is therefore also the correct behavior
In which case, "expressly tell folks not to run HBase on top of LocalFileSystem," is the correct action on your part. People must not be using the local FS as a direct destination of HDFS output.