My SA told me that they do get commission and also have quotas beyond that. So if your SA calls another store and gets something for you the SA shipping the item from that store to your store gets the monetary commission but the quota tally goes to your SA. I can't say for sure if Kellys and Birkins count on this but my SA has always acted like commissions are appreciated from any sale be it a Kelly or a Bolide.
On the main issue, I would definitely walk in and show of the Kelly. There is no harm in your getting it elsewhere and it may improve your service even further as it proves you are a real lover of all things Hermes. My SA has never begrudged me purchases made at other boutiques or resellers although he does cringe at ebay due to the fakes threat issue. Lets face it, not all boutiques have a ready supply of the perfect leather and style so we need to grab what we can when we fall in love and shouldn't be penalized for doing so since Hermes itself doesn't readily stock Kellys or Birkins or any style that comes bo mind in every color combo under the sun.