Conversely, love him or hate him, he was an intelligent man. And he clearly understood logistics. How did it not dawn on him that the estimates just didn't make sense?
So to speak to this specific issue - how did it not dawn on him that the estimates just didn't make sense.
The problem is that they actually
do.
As I noted, by the end of July there were 2419 companies of Confederate troops (infantry, cavalry or artillery, with each artillery battery counting as one) either at Richmond (2158 of them in the actual Seven Days, 261 having arrived since) or with Jackson's force that had moved to the north after the Seven Days.
The actual estimate for the strength at Richmond, plus Jackson's force, used internally was 252 regiments-equivalent (i.e. 2,520 companies), with the excess resulting from double counts.
This should by itself indicate that the numbers involved are
not fundamentally implausible. They make sense, because the Confederates can get very nearly that number of
regiments to Richmond in the sense that they are not being used anywhere else and can physically travel to Richmond.
The arrival of Beauregard's force (the separate, dubious 20,000) was a persistent rumour that McClellan kept getting from contrabands and could not rule out, but the means existed and they had not been localized anywhere else. (The source of this rumour was that Beauregard had arrived in Richmond.)
Do those regiments translate to the numbers that McClellan used?
Well, 252 regiments at 700 Aggregate Present per regiment gives 176,400, which is near enough the 180,000 used. McClellan's own strength at this time is about 175 regiments of all arms, and his per-regiment AP strength is in that ballpark.
Now, the next question is - why would the Confederates be concentrating this much strength, and is that plausible?
To my mind, the answer is - yes, it makes sense for the Confederates to concentrate this much strength if they can. It represents the worst case scenario for McClellan's own operations, but it makes strategic sense that the Confederates would concentrate everything they could muster to drive the Union away from Richmond (as in fact they actually historically did, mustering - as noted - over 215 regiments of all arms at Richmond for the Seven Days and another 26 regiments arriving afterwards.) This is because the loss of Richmond is bad for the Confederates strategically in several different ways, and because no other Union campaign in June 1862 offers anything like the same strategic threat.
In addition to all of the above (which indicates that there are good reasons why McClellan would think the Confederates would be both able and willing to do this, and that they in fact in large part
did do this by concentrating all disposable forces at Richmond), it's also worth pointing out that the context also gives good reasons why McClellan would want to raise alarms about this possibility. As of May and June, the Union administration appears to be taking the view that McClellan has ample men to do the job - or that there are other operations that it wants to do which are of at least equal priority. It has promised McClellan reinforcements and then denied them to him, and as of June 20 there are about 90,000 men PFD in the East who are
not in McClellan's army (despite McCall's division being sent to join him).
In this light it would make sense for McClellan to be pessimistic, though any incorrect assessments appear to have resulted in an overestimate of enemy strength of about one third (some from excess regiments, some from Beauregard) and this is actually not as much as in other known cases of overestimation.
The final point to make, though, is that the only real way in which an incorrect force estimate matters is if it leads to fundamentally incorrect decision making on the part of the one who made the estimates.
There are two things that happen during the Seven Days where it would be possible to argue McClellan committed an error about force allocation, but of these one is definitely not "there are too many enemies" and the other is probably not.
The first one is the amount of reinforcements sent to Porter. McClellan could (it could be argued) have pulled back into his defensive works, surrendering his gains from the 25th-27th, and sent more forces to Porter.
However, the forces actually sent to Porter appear to have been about right. The line broke thanks to bad luck towards the end of the day, and this bad luck event could have happened even if there'd been more troops to the north; more to the point, McClellan not sending enough troops to defend his supply line and maintaining a more offensively oriented position south of the river is hardly the sign of someone who thinks he's too heavily outnumbered.
The second one, which is complimentary, is whether or not McClellan should have
attacked on the 27th south of the river. However, actually south of the river at the time (Magruder's defensive forces) were about 800 companies, which equates to about 80 regiments and thus to a bit more than two of McClellan's normal corps. (5th Corps is bigger, 4th Corps smaller, the other three are about 300-350 companies each.)
I feel that it's not really solid to argue that the forces McClellan left south of the river could have just rolled over Magruder's defensive force. Consequently, the idea that McClellan overestimated Confederate strength and thus missed out on an opportunity to attack Richmond on the 27th is to me poorly grounded.
As such, I think that the estimates were within the bounds of what could reasonably be estimated based both on fundamentals and on the information available, and that they did not drive McClellan into a fundamental misstep in the Seven Days. If anything McClellan's error in the Seven Days could be said to be that he was too aggressive, and that he could have avoided being forced away from Richmond by covering (ed: Tolopatamoy) Creek, but this would mean giving up his assault concentration and so he'd just be in a stalemate.