If I understand, a guide such as the one you suggested would include one set of references for alternate unit designations. There must be many cases in which records of soldiers who belonged to one unit may be filed in more than one place. So, whether we agree with War Department clerical decisions or not, there should be another set of references to let people know how the records are filed.
Of course it would greatly facilitate many research efforts if we knew the county (or counties) of origin for each company. Add a summary of the unit's history and assignments, and you've got a useful guide to Arkansas Confederate commands!