The IndexScrutinyTool relies on doing point-in-time scans to determine consistency between the index and data tables. Unfortunately, deletes to the tables cause a problem with this approach, since delete markers take effect even if they're at a later time stamp than the point-in-time at which the scan is being done (unless KEEP_DELETED_CELLS is true). The logic of this is that scans should get the same results before and after a compaction take place.
Taking snapshots does not help with this since they cannot be taken at a point-in-time and the delete markers will act the same way - there's no way to guarantee that the index and data table snapshots have the same "logical" set of data.
Using raw scans would allow us to see the delete markers and do the correct point-in-time filtering ourselves. We'd need to write the filters to do this correctly (see the Tephra TransactionVisibilityFilter for an implementation of this that could be adapted). We'd also need to hook this into Phoenix or potentially dip down to the HBase level to do this.
Thanks for brainstorming on this with me, [~lhofhansl].