Bad example with fast food. If a customer just buys burger and fries, the place made less money than if they get combo, which is probably another $.50 on top of burger/fries, because the drink costs store about $.05. So while combo was cheaper, the store actually made more profit.
There is no ingredient in homebrewing that has such a huge markup to result in a similar situation. Certainly not hops or yeast.
With a kit you are paying for convenience hands down, as well as benefit of only getting the amount of hops you need, when they are usually sold in 1oz increments. Have you heard of meal delivery website like blue apron? The markup is huge, but you can justify 'saving' because you don't have to buy a whole container of a specific spice you've never used at $6 or an entire bunch of celery, you just get the 2 tbsp or the single stalk you need for the dinner.
Same idea with a kit. I have a brew I'm about to make after a long hiatus with quite a few hops at 1/2oz and even one with 1/4oz. Well I have to buy an ounce of each of those. If I don't use what's left over, that cost needs to go into my 'a la carte' price to compare apples to apples. With a kit, I would get exact.
I don't know how your LHBS can sell the kits at lower than a la carte, as it takes time for an employee to assemble the kits, there is packaging involved, etc. Unless they use their bulk unit price to come up with cost of kits. So if kit has 1 oz of cascade, they would only add $.50, vs. $2 or whatever for a single 1 oz package of those hops. Same with grain, their bulk sack unit price is a fraction, probably 30-40% less, of their unit price sold in bins. 15 pounds at bulk is $15 or less, but out of bins, probably $25.
That is the only way they could kit something less than a la carte.
My LHBS has a cool deal where you pay for a bag of grain, say $50 for a 50 lb of 2 row, but you don't take the sack, you just have 50lbs worth of credit for 2 row in their system, and every time you go and get 2 row, they update what you have left. However many trips it takes you, doesn't matter. So you get fresh grains, but at bulk pricing.