Is the composition of the companies that made up the 3rd and 4th reserve regiments, and the 3rd and 4th reserve battalions, known for sure? Specifically, could these companies originally have included a mix of juniors and seniors, as you mention, or could these regiments or battalions originally have included a mix of junior and senior companies?

If so, perhaps, after the 3rd and 4th reserve regiments were formed, the juniors (or junior companies) were detached and placed into battalions, which were then referred to as the 3rd and 4th reserve battalions, based on the regiments from which they were formed. Perhaps these were then planned as the basis for the 64th and 65th regiments.

The 3rd and 4th regiments would have been left as battalion-sized senior regiments, and perhaps were then referred to variously as the 3rd and 4th senior reserve regiments or the 3rd and 4th senior reserve battalions.

This might explain all the confusing references to these units. Below are some accounts [by Federal captured at Athens in September 1864] of junior reserves being among the guards at Cahaba, which may be evidence that the 3rd included some juniors:

James W. Wells, Co. B, One hundred and second Ohio Infantry: "The guards about the prison were composed of the meanest grade of soldiers, all being either old men over 60, or young boys under 16, considered unfit for active service in the field." [History of the 102d Regiment, O.V.I].

Hosea C. Aldrich, Co. G, Eighteenth Michigan Infantry: "I shall long remember the looks of the sandy headed boy who stood guard at the door that we passed through to go into the cook yard." ["Cahawba Prison, Alabama," Camp Fire Sketches and Battle-Field Echoes of the Rebellion]