You don't need a modified thinset to put down the cbu on the floor (this thinset doesn't actually hold the cbu to the floor- it fills in any imperfections and makes a fully supported substrate for the tile). For actually setting the tile, it somewhat depends on the type of tile...a modified thinset (one that makes it stickier and stronger than 'plain' thinset) can also be more flexible and help prevent cracks. If you are setting stone, or very large tile, or the floor is not flat, then you might want a granite and marble medium set (it has more sand in it to help prevent the big tile from sinking - it can be used typically up to about 1/2" thick, where normal thinset is usually only good much thinner).
So, that still didn't answer your questions, but hopefully helped some. I strongly suggest you check out www.johnbridge.com They specialize in tiling, and you'll ge a good quantity of tile professionals to help you out with your specific questions.