1) No, you can have the Phottix transmitter in your camera's hotshoe, and have another flash in the Phottix's hotshoe on top. So you'll have the remote flashes as well as an on-camera flash simultaneously. Theoretically you should be able to have as many remote flash receivers as you want. It looks like you can create up to 4 "channels" as ways of separating the remote flashes for different purposes.
2) In theory, you want the versatility to NOT have to have your on-camera flash go off in order to trip the other flashes. In practice, you can set your on-camera flash to like 1/128 the power of the external flashes, so it's a non-issue, as the light from the on-camera flash is 7 stops darker than the external flashes so you'll never see it anyway. Also, it may be possible to have the on-camera flash act only as a controller and not go off itself when triggered. I'm not sure, and it probably depends on the brand and possibly the specific model of flash.
In general, I would say go for the Phottix unless you can confirm that the Sony unit will do exactly what you want it to do.
On a different note, just being able to use the flash "off camera" can be more cheaply achieved by a simple cable setup. Of course then you are limited by the length of the cable. It all depends on what you're trying to achieve. But even a 2-3 foot length can be good if you're just trying to add a little character in the shadows and keep from having the deer in the headlights look from having the flash direct on your camera (you can hold the flash in your left hand to position it in different ways). But if you're going for full off-camera freedom, then you will also probably want a light stand and an umbrella. The light stand for placement (usually you will want the light at head height or higher.... it can be tough when you're limited to environmental things like placing it on tables and shelves and stuff) and the umbrella to make the light effectively bigger to soften the shadows.