Oh I see what you mean.
Technically from 3 weeks they were free to come and go as they chose - but I don't know that they spent that much time on the coop floor until about 4-5 weeks - but then they definitely did spend time on the old litter.
I think the theorists would say that the ideal thing would be to give them exposure in small doses rather than a full onslaught - so they can develop their immunities.  Practically that might look like running around for a few hours during the day but still having their own environment for the rest of the time.  I have never heard of anyone doing that in practice but it probably is the ideal 'integration' into their new microbiological environment!
		
		
	 
Well, with broody raised chicks (at my place, anyways), once momma takes them out of the nest box (1-2 days), I put them in a plastic dog crate or my mobile broody house [Edit to add:  my coops are raised, so really young chicks can't get back into the coop once momma takes them out - hence the dog crate and or broody pens - that are on the ground]....and erect a wire dog pen around it for a few days...so they have clean bedding in the dog crate, but the regular bedding from the run in the pen.  Once they all 'have their legs under them ( just another day or two after moving to the crate), I open  the pen gate and observe to see if momma can/will protect them.  Sometimes they end up in the 'see don't touch' for another week (depending on mom, how many chicks she has, and when they hatched relative to the weekend (i.e. when I can observe))
After that, one of two things happen - they are free to interact completely with the flock, or a create a 'creep' at the entrance to the pen, so they can go in and  out at will, but the bigs can't fit in (this also means mom is stuck inside the pen/crate complex - which I don't like, so I ONLY do this if I need to for the safety of the chicks - which is not often relative to the number of mommas with chicks.
I do make sure the run bedding isn't disgusting....like after a number of rainy days...but otherwise, I think it is good for them in the sense of building their immunity. In the wild they would be with the flock as soon as momma left the nest.  The only difference being that there is not the concentration of chickens per space in the wild like there is in our penned flocks...meaning there is the potential for higher pathogenic load.
So far, I haven't lost a chick to illness/failure to thrive - other than ones that passed within 24 hours of hatching because they were weak or something was wrong with them.  I have lost a couple to momma (see this week's synopsis) and a couple this summer to rats (No, I haven't managed to defeat them - in fact, I am sure they are growing in number, as I now see them - usually younger ones - out during the day.  

)
So, I suspect that the best strategy is somewhere between mine and Bobs???? 
 
   
   
   
  
   I really don't know.