IMO it's probably best to go for the design the manufacturer intended.
I've used a rubber hood on my nifty and that worked well enough but there is a concern that it puts stress directly onto the moving parts of the lens mechanism rather than attaching to the solid outer barrel of the lens. You may need to be very careful when fitting any hood directly to the innards of the lens rather than the barrel. A rubber hood can be very handy when shooting through glass, when its flexibility might help you completely seal off spurious light sneaking in at the sides. Sam-D has already made valid points about convenience.
As for petal vs "full", a zoom lens is more likely to have, and to need, a petal design since the cutaways are important to accommodate the wide angle end of the zoom range, while the longer the hood can be, the better to serve the telephoto end. Unfortunately, with a zoom lens you can't serve both purposes optimally. A properly designed petal hood is the best compromise you can hope for when using a short to medium zoom lens.
For a short prime a petal lens would theoretically offer optimum performance but the Canon hoods I have for my 50/1.4 and 85/1.8 are both "full" designs, not that there is much to either one.
For a long prime, or even a long zoom, such as the 100-400, since there is no real wide angle involved, the hood design simply as a long tube is perfectly fine.
What you will find with OEM hoods is that they are lined with black flock/felt and that will help absorb light coming into the hood and may also trap dust rather than letting it settle onto the lens. Cheaper eBay style hoods may simply be bare plastic and not quite as good at minimising reflections. They'll still afford good protection against physical knocks and splashes and will probably help reduce flare as well. The fit may be good, or poor and I guess it's pot luck whether you get a good one or not. I have bought a couple of knock off hoods but one of those broke and I've replaced it with the proper Canon model, which has the flock lining and which I hope will prove more durable.