I thought that they had to set up a different system for retailing their product if they were they manufacturers and distributors of that same product.
As other's have noted, your thinking is incorrect. Manufacturers often WILL set up a different system for retailing their own products, but they do that to avoid competing with and offending their current customers (the distributors), not because they have a legal obligation to do so.
By controlling all aspects of production, distribution and marketing couldn't they inflate the product to the point where it didn't reflect the true market value?
A manufacturer may charge whatever they want for a product -- if they charge a price too high, the market will stop purchasing the product. What the manufacturer cannot generally do is dictate minimum prices that the distributors must sell at. The manufacturer can suggest retail prices, and can raise the price to the distributor, or stop selling to the distributor, if they don't sell at retail price. The manufacturer can stop selling to a distributor if they don't like their distribution methods. Basically the only thing a manufacturer cannot tell it's distributors "you must sell the things I manufacture for $X."
There are fewer controls over "vertical price fixing," which is the manufacturer -> distributor -> retailer chain, that there are over "horizontal price fixing," which is all of the retailers colluding to raise prices.
Isn't that what anti-trust laws are supposed to prevent? Didn't Microsoft get into trouble for something like this? And then ended up having to pay fines?
No, the Microsoft case is completely different. MS did not get into trouble for horizontal or vertical price fixing -- they got into trouble for using their market power ot maintain their monopoly. Monopolys, contrary to popular belief, are not in and of themselves illegal -- what is illegal is using anticompetitive means to botain a monopoly, or using "market power" to maintain a monopoly. MS got in trouble because it used its monopoly powers to keep competitors from entering the browser market. It's the anticompetitive use of monopoly power that is illegal, not gaining or having monopoly power in the first place.
Are companies allowed to say that you can not discount their products for sale online?
Sure. Companies can say you can't discount on line, you can't advetise prices online, you can't sell online, whatver -- as long as they don't demand that you sell at a minimum price, they are in the clear. Companies can do all sorts of things that make it so that effectively you do have to sell at a minimum price, but that's legal -- really the only illegal activity in a vertical supply chain is somebody requiring a minimum price.