Rest after they take Moscow and no, the Mozhaisk defense line didn't collapse until the end of October.I'm not sure what you are suggesting at ATL you first off start by saying break through the Mozhaisk defense line but this is what they did mid Oct anyway (it's just their logistics and road conditions and teh fcta that were worn down meant they couldn't press on). But then you say mid Oct they should rest and consolidate and stock pile?
But you can't do both?
The routes of attack into Moscow were on all weather roads but, anyway, the Germans did continue the attack anyway, finally collapsing the Mozhaisk by the end of October.Either way your problem for either is from early Oct the roads are turned to mud "rasputitsa", so attacking is hard and so waiting and resupplying is not guaranteed. Nw in OTL they went with attacking and broke through but still could move in, when the ground froze in Mid Nov the mud issue started to lift (but of course the cold brought it's own problems although how much is debatable*).
The Russian civilians could make all the defenses they wanted; it wouldn't matter because the Soviets at this juncture didn't have the men to man them. As I've said, the only troops within Moscow at this time are few NKVD detachments not suited for fighting for the city, and were currently engaged with trying to keep law and order among said population. As for said Muscovites, I presume many would flee, as Wiking has pointed out but given the German proclivities in terms of Soviet populations, I'll doubt they'll be much of an issue.Zhukov also started fortifying Moscow from the moment he takes control on the 10th Oct, yes it's initially with a quarter million civilians digging trenches and tank traps and fortifying buildings but the idea that Moscow was defencelessness is kind of overdone IMO. Now long term such actions won't keep a determined well supplied and large German assault out but it doesn't need to because at worst it just has to buy time. Plus you don't have a well supplied German force to keep at that time. There's I think an underestimation of what is needed to take an hold a city of 6m people even without large numbers of red army in it, Moscow is big, way bigger than any Russian city they've attacked so far (hell it's bigger than any city the Germans attacked full stop)! Plus it's the wrong force to do it anyway, Panzers and mechanised panzer grenadiers are not what you want for this. You want all those infantry divisions who are stuck in the mud back down the line, which is why in previous encounters with cities the Panzers tend to bypass then but hopefully cutting them off from resupply and the following infantry moved in to take them and pacify them.