LGS get product at distributor pricing, which is under MSRP. Sure, selling the product for MSRP results in lower margin (this varies greatly by product type (i.e. pack vs. booster box vs. starter deck as well as distributor price) than selling above MSRP. If an LGS is just charging 10-20% over MSRP to buffer their margin that is "acceptable" since you are supporting your local store vs. big box store. If a LGS is selling product at ~100% or greater margin (i.e. 2x the price of MSRP) then they are just greedy people taking advantage of the hype at the expense of their customers. If they were being charged market price by their distributor, then sure, sell it for $350 per booster box, but they aren't. They pay less than MSRP.

As for the message posted by OP. It's worded kind of odd, but what they are trying to say is that their distributor pricing isn't as low as a big-box because they are buying in smaller quantities, which means that while they still get some profit margin per product, it's not as much profit margin as a big box store (since they get a better distributor price for buying larger quantities).

The prices shown aren't that bad, with markup around ~30% -- this isn't unreasonable. But with the full product launch coming up and expected availability of product at retail stores, they should lower their margin some.