Plenty of companies (including manufacturers) have Amazon storefronts. Some of them use Amazon for fulfillment, some just use Amazon as a storefront. I don't see why MSI can't.
While Amazon's site for computer parts isn't nearly as good as NewEgg's (Amazon's spec search capability is pitiful), I've never had any difficulty telling who the seller for a particular product is. In your case, if it said "Sold By: MSI", you can be pretty sure that's who it was.
As far as not getting a shipping quote until checkout? That's pretty normal for lots of web stores. If you are going to charge for shipping at all, per-item shipping is certainly a choice, but plenty of web retailers do it differently. They can go by actual shipping cost, a rate based on total order size, etc. In Amazon's case, if the item is fulfilled by Amazon, you either go with the free shipping (or prime), or you pay according to their published shipping rate tables. If it's not fulfilled by Amazon, they just do whatever the retailer tells them to.
Personally, I find NewEgg's shipping to be the most confusing: depending on the individual item, shipping is either free (and slow), free (and less slow), per-item, or total-weight. And it's never clear which shipping rates are going to apply if your order contains items in multiple shipping categories.