Actually due to the price hikes involved near the end of 1.0, and the price changes going to 2.0 I noticed many shops that stock DDM lowered there profit margins by a few dollars not only to keep people buying the minis as boosters, but also compete with other stores.Most of what you state is true, but the profit margins are mostly the same. Retailers get the roughly the same reduction in price from the distributor per MtG box as they do a case of minis.
Some products will have a different % reduction. GW's LotR miniatures game has a smaller reduction in price to the game store. The explanation from GW is that they have to cover the royalty fees they pay Tolkien's estate.
The over all reduction in price is usually based on the total volume the store orders from the distributor.
Thanks,
Rich
The price increases for CCGs aren't that great, and extra quarter here or there, and the overall mark-ups were something in the range of 33% for CCGs and 26-27% for CMGs.
Sometimes even more for CMG's to get the older ones off the shelf to make room for the newer, less space taking, and quicker selling CCGs. So the CMGs may go nearly at cost or only about 10% mark-up sometimes because the overhead was too much.
Consider a booster case of minis is 12 packs, and a booster box of CCGs is around 24-36 packs depending on the game, the cost of CMGs nearly requires you to mark-up to about 40% to be able to get back all your costs which people would not pay. For a CCG booster box to cost the same as a CMG booster case it is a no brainer to stop carrying so much CMG and carry more CCGs.
So even with the same 33% mark-up a store is making less profits on CMGs than the CCGs. That is IF the store can sell a CMG for the regular mark-up or MSRP.

Don't get me started on LotR, as there is much more to them and other games than GW will not actually tell you. For example their price fixing agreement many people must still sign to be able to carry there products, not to mention the base product line you must carry including LotR even in an area where people may not play it. If you don't have the LotR on the shelves if/when a GW rep may pop into your store, your account is canceled to purchase more GW products of any kind.
Anywho, this has little to do, but some with the DDM so lets leave GW alone and just that ALL minis games cost a store owner more than it looks on the outside and bring in little to no profits because of it. CCGs is where the money is now for MANY reasons to both stores and players. CMGs are slowly dying for every company, and the ONLY way to keep their heads above water is with massive prize support for anything mini related to get players in to buy the minis products.
Retailers also don't always get the same "discounts" as some don't even get product they ordered because distributors have a favoritism system as to what retailers get product first no matter when it was ordered. Diamond Distributors/Comics, Alliance Games, etc all do this be it CCGs, or minis, or anything else! So discounts are based on quantity you buy, in addition to IF you are allowed to buy something to begin with if you are high enough on their "preferred customer" lists. Only getting directly form WotC do retailers get a fair shake, and WotC doesn't have enough stock to supply everyone directly as the wholesalers have.
At least that is my experience with it all, YMMV