Don’t go crazy about bodies. It doesn’t seem to make the base go on full alert, or at least not immediately. Do NOT risk getting seen to hide a body. Just don’t get seen in general
Make sure that you scout everyone in the base before going in. Even if you get spotted, as long as they aren’t near enemies, you can generally kill them without raising the alarm.
I’ve found the stealth to be pretty forgiving for the most part, although sometimes you will just have bad luck and some big bases are quite hard. This is certainly no Metal Gear Solid game.
As far as knockdowns, i’ve found that some attacks stun you so you can’t dodge out of them while standing or on the ground. I’m not sure which ones do this, but i know that every hit from certain late game boss enemies stuns you so that any time one of them hits me once, i will get struck by a combo that does half my health. Later on some normal enemies can do this too.