I'm not sure I understand your "metric" and I don't think many people do, either. Apple is profitable, and we can leave the "big" or "small" determinations based on total number of employees. What you consider as "fodder" (Apple store employees) also enables Apple to have unparalleled retail reach which is key to their strategy & sales, which makes them profitable.
I'm not sure I follow what your point is, maybe you can clarify it for us.
What makes a company valuable?
1. Physical Assets, plants, trucks for shipping, warehouses, etc...
2. Intellectual assets, smart people, patents, licensing agreements
3. Cash/liquid assets
Apple is strongest in 2/3. I bet their physical footprint is at the bottom for companies of similar market cap except for Google.
Their intellectual assets make them big, but the Apple Store is a model and its meant to shove anyone into that model and see if they work. I've been in a lot of Apple stores on regular basis, their turn over is decent. Apple store employee's are not an intellectual asset, the program and model may be, but not the employee's.
Take the Apple store employee's out of the mix and what do you have left? A strong intellectual core and a lot of cash with not much in the way of physical assets.
I'm not saying its bad, in fact its very smart, but for the purposes of comparison they are a small company.