When in the PAL Wizard and exporting a selected threshold file to a Perfmon Template, yes, it includes the counters from all of the threshold files that the selected threshold file inherits from.
Yes, when a counter log is presented to the PAL tool that has all of the counters needed by the selected threshold file and the inherited threshold files, then the selected threshold file and all of the inherited threshold files are merged together and analyzes the counter log. All counters in the counter log that match the merged threshold file should be in the report. Keep in mind that some counter instances such as _Total are ignored in the LogicalDisk and PhysicalDisk counter objects, so all instances of those counter objects need to be recorded in the counter log data recorder.
Yes, when a counter log is presented to the PAL tool that has all of the counters needed by the selected threshold file and the inherited threshold files, then the selected threshold file and all of the inherited threshold files are merged together and analyzes the counter log. All counters in the counter log that match the merged threshold file should be in the report. Keep in mind that some counter instances such as _Total are ignored in the LogicalDisk and PhysicalDisk counter objects, so all instances of those counter objects need to be recorded in the counter log data recorder.