Be aware that a lot of people don't like optics for various reasons and show their prejudices in their recommendations. Both have their trade-offs. The right optic can be very good for some purposes. Like when trying to illuminate a distant object with close objects near your line of sight that too much spill will light up and cause glare dimming your sight of the far object you actually want to look at, you can use a narrow optic with no spill. Optics come in more beam variations than reflectors do, so you can swap out for a flood beam or narrow spot with no spill and anywhere in-between just by changing the optic. I do this with my SF L1 and Minimag all the time.
So on to your questions......
*You should cover the optic with a glass or plastic lens/window JUST LIKE ANY REFLECTOR to keep it from getting damaged. Optics and reflectors are the same in this respect. Smooth front optics CAN be used without a window, may get scratched, but cleaned off OK and still be used. I have one light with an exposed optic and it has been fine so far. They are made of acrylic which is not hard, but not soft either. They can take mild punishment, just take care not to scratch the back while installing it.
*The holder is supplied as an aid that reflectors never seem to have, but also sometimes need, so this is an advantage, not a problem. The outside shape of an optic and reflector are very similar, so an application that needs an optic holder probably also could use a reflector holder (but none exist). Most often, an optic or reflector of appropriate size will drop in to a flashlight bezel and either be captured between the LED and lens (automatically centered if placed on the emitter during assembly), or be captured and centered by the bezel (usually also centered). I have many optics, no holders, and don't miss or need them.
Caution: metal reflectors can cause shorts if soldered connections on the cree pad are not kept low and out of the way. This is not an issue with optics or plastic reflectors.