Pulsefire got its own category because of the features associated with it.
Most legendary skins change how the champion acts (voice, spell, etc), while Pulsefire changes not only Ezreal's appearance, but other champion's animations as well. Enemy champions and minions killed by Pulsefire Ezreal have a unique death animation.
In addition to this, the skin itself evolves and changes its appearance further as you level up Ezreal's ultimate.
There is actually a very interesting post on the League of Legends forum explaining some of the design choices, including a developer commentary on the creation of Pulsefire Ezreal.
In addition to this, it adds a new Profile scheme as mentioned by Patrick Stadler.
Also, in lieu of more text, have this cropped photo of Ezreal's crotch along with a description of all of the features involved in his theme:
As for whether or not the Themes will periodically be placed on sale, there is currently no answer. My best guess would be that they are going to be similar to Legendary skins in that they do not go into a usual sale cycle like regular skins. Only time (and a few additional Theme releases) will tell.
Yes, along with any free skin there is always a free champion that comes with it.Very much similar to how server transfers may gift you a welcome skin and champion. e.g gladiator draven and pool party ziggs.
Best Answer
I couldn't find any offical FAQ answer on this, but obviously rerolling 3 legendary shards does not automatically result in a permanent legendary skin. Here's a counter-example where the player is rerolling Alpha Battle Skarner, Battlecast Prime Cho'Gath, and Project: Yi (all of these are legendaries) and it gives a permanent Dragonwing Corki (regular permanent skin).
Also, this reddit post and LoL Boards post tell that rerolling skin shards is random. You can get a 520RP skin from 3 Leggy's and vice versa. This is, of course, all experience-based, but finding counter-examples is enough to answer this question.
So my advice would be to disenchant high-value skin shards into orange essence, and to reroll the low-value skin (520 and 750RP) into permanent skin.