Yes, you can use whatever you want as a substrate. Gravel is just cheaper than the eheim ehfilav. Of course, perhaps you should use it in the canister where it will be more effective. YMMV.
Yes, but would not be as efficent because the amount of water flowing through it. In your canister you get 350 gph so it becomes more effective. Your regular gravel actually has beneficial bacteria growing on it.BB will grow just about anywhere in your tank.
Yes anytime you clean any part of your tank you will be removing a small amount of BB. Luckly we have well designed areas to grow strong BB colonies and then force the tank water through that area.