Ok, so when you boil the water the fluoride is indeed concentrated in that water that is left in the container. HOwever, the steam is pure, fluoride free, water. so any distiller that uses steam condensation creates pure water. Reverse osmosis on the other hand removes anywhere from 85 to 95% of fluoride, depending on who you believe. but it depends on how good the filter is.
so it sounds like the crystal water machine creates steam distilled water, which would be fluoride free. however, there is likely some fluoride residue left in the unit when its done, so giving it a good cleaning now and then might be a good idea.
the water experiment you linked is cute, and I have seen it before, its made its way around the internet. It certainly illustrates the concept of the damage microwaves can do, as they say a picture is worth a thousand words.
well, anyway if you do decide to create any type of experiments with the water let us know. it would be interesting.