With regard to the $5 per license, you have to bear in mind that you also have the administration of the encoders, and while the costs are relatively low, it is a standard business model to include a profit not only to cover costs , but also to include ..... shock ...... horror ....... profit. There may also be exchange rate variations to take into account as well, all of this could quite easily reach 3-4 times the actually cost of the license.
You pay for this once, whereas other people think it should be thrown in free, even if this did cost Cakewalk $10 to include that with each sale, and they have 1000 sales worldwide, thats $10,000 cost over that perio. Research to see how much actual profit that Cakewalk make, and you will find that this is a sizable chunk of money for them.
Rather than charge you for it they give you the opportunity to buy it once for all the products (actually saving you money), they also give you the opportunity (and even tell you how) to do it for free. Either of which is preferable to them bundling it with everything, and the consumer having to pay for it with every disk sold.
Also Im curious to know what other professional audio software includes it, I certainly know that Cubase Essential and Cubase Studio do not include it. I wonder if Pro Tools has an mp3 encoder?