Well, I think you have a point - that it doesn't really make sense for the 101 to refer to the flesh cover - but this detail has been appearing on toy boxes now for years. If memory serves the boxes of the old Sideshow 1/6 figures went into a lot of detail about it. It hasn't been contradicted by any of these actual movie writers like Cameron and Fisher...or Wisher, can't remember his name - the people who know what was intended.
As I said though you make a good point - if the model number refers to the flesh cover and the resistance knows these model numbers and the particular flesh cover that they refer to - then Skynet's ''infiltration'' is busted. On the other hand if the resistance only finds out these model numbers at the last minute, like when they are just about to send Reese back through time, how does Reese even remember that little detail. Not impossible that he could but less plausible than if they'd known it for a long time. And at Tech Noir couldn't Reese have spotted the 'model 101' a bit before he was actually on Sarah with the gun pointed at her head? Incidentally Sarah should have been dead right there. A real machine wouldn't take a dramatic pause.
I never get sick of looking at it this way. 
Here is another one I took on the same day.
He is still one of the best figures ever made by HT. 
