The idea that the AOP enjoyed more coherence and less straggling or desertion than the ANV is widespread but counterintuitive. Saving the matter of numbers for a later post, let's first apply some general observations and reasoning.
Management of the AWOL problem - Here's a question; notice your "gut instinct" in answering it.
Which Civil War side's high field command, Union or Rebel, best matches the statements below:
* Mindful of the AWOL problem, distressed by it, harshly suppresses it.
* Inattentative to the AWOL problem, blase about it, soft on punishment.
On the one hand, we have the Jackson/Lee record of dealing with stragglers, worrying about the phenomenon, safeguarding evry march against straggling, even executing laggards. On the other hand we have Marsena Patrick collecting dawdlers roadside and returning them to their units.
The seriousness with which the ANV regarded straggling could have come in whole or part from worries about Union numbers; the anti-straggling, anti-deserter harshness might have exacerbated the problem; or, the commanders might have been making a mountain out of a molehill. The attitude itself does not point to higher or lower straggling, but to a commitment to fight it through the most desperate measures, including firing squads or hanging.
We should note that the Rebel commanders' actions were aimed at the reduction or elimination of the problem. There is not public Union equivalent to the record left by Lee on this, nor to the actions of Jackson on the march. Union commanders made fewer efforts, milder efforts to correct their problems. My bias is towards assuming less control of the phenomenon on the Union side and therefore more problems.
Content of anecdotes - In surveying the anecdotes about stragglers and deserters, one is struck by how out-of-scale Union stories are. In researching this post, I noticed Joe Harsh gave one example to support his claim of higher ANV straggling rates. IIRC, a small party of three or four rebels announced to their company that they were going to the rear to brew coffee or cook rations as a battle was pending. At the end of the day (and fighting) they rejoined their unit.
Meanwhile, on the Union side, Wainwright tells of a march in which he sees "thousands, literally acres of them [stragglers], cooking their coffee or sleeping around their fires."
Consider the the hundreds of stragglers who seized a medical evacuation ship sent to the Peninsula, the Daniel Webster; the chief sugreon then counted another 1,200 stragglers who had been skulking in the hospital who failed to make their getaway! This at a time when the surgeons counted an AOP present-for-duty strength of 78.000.
Structural bias - One kind of anecdote on the Rebel side that I should mention is that of various Southern localities developing armed bands in the bush, some of which waged war against local authorities. That speaks of a high desertion rate. However, in reading The Free State of Jones, one notices that the manpower in these bands also consists of Unionists, outlaws, and escaped slaves - not just deserters.
The South's ad hoc desertion - whatever its rate - had a structural equivalent on the Union side that is not widely understood.
Union soldiers wrangled "gray market" furloughs from company grade officers. McClellan or Hooker might have a ban on leave or a requirement leave be given by regimental commander or higher, but company officers could stand on state authority (however they interpreted it) and give furloughs at will. Equipped with these dubious passes, soldiers had only to finagle their way past those few checkpoints answering to a McClellan or Hooker and they were "home free" with "legal" authorization and full documentation. Moreover, these getaway artists remained on the roster to show up on the payroll musters monthly thus bamboozling muster-loving pop historians as well as their own high commands.
As we have seen, Lincoln attributed the AOP's low participation rate mainly to these furloughs and it would be interesting to try to estimate the dimensions of the problem. Surely, Hooker's rebuilding of the strength of the Army after Burnside owed much to recalling soldiers who had gone home on company passes.
In sum, the Union had a vehicle that facilitated absent with leave claims for many who were in fact AWOL. On the Southern side, there is nothing like this and army-level leave policies (like McClellan's) seem to have been strictly enforced below Lee's level.
In light of just these three considerations, I have great difficulty accepting ANV AWOL as being higher than that of the AOP.