From what I’ve seen here, it would appear that the danger comes more from “overdoing” it than from doing it in the first place. It might not even be done incorrectly, but rather *too early*.
As far as pumping goes, there are numerous threads out there that discuss how much pressure in a pump is too much. Even if more feels comfortable, don’t go higher, because the damage occurs before it starts hurting.
Jelqing manually hasn’t caused me any problems, nor for anyone else I’ve seen, since you have a pretty good idea of how hard you’re squeezing when you use your hand. When you get or build a Powerjelq/canning tong jelqer/drumsticks or whatnot, you have to be very careful that you’re not squeezing too hard, because those mechanisms do a lot to multiply the amount of pressure on your penis over what pressure you feel in your hand. Just keep an eye on what you’re doing, and you should be okay.
I don’t have a lot of experience, but what folks say around here about doing the newbie routine makes sense. They say that you should do the newbie routine for a couple of months before involving mechanical doohickeys, as it will limber up the penile tissue and make it less susceptible to major damage.
It would make sense that a lot of the injuries you hear about from the more advanced “tool-assisted” exercises come from failure/negligence to do a newbie routine. Think of it this way: if a morbidly obese man decided he wanted to get in shape, and chose to start by doing 300-yard sprints up a 30-degree hill, he’d probably die of a massive heart-attack before he finished his second ascent. But if he starts by taking fairly leisurely walks around the block, maybe throws in a few body-weight squats daily after a couple weeks, and adds uphill *walking* for a couple weeks after that, he’ll be far less likely to have such problems when he moves up to the sprints.
They call PE exercises “exercises” for a reason: they’re a true workout involving stresses on bodily tissue. Don’t throw too much at it right out the gate, or you might seriously hurt yourself. But if you slowly break yourself in, there should be far less chance of breaking yourself entirely.
As for your question about doing BC/BS flexes, yes, that should do something to counteract injuries, as it is a basic exercise that will increase blood flow, and thus allow tissue repair to occur more quickly. You should be doing those even if you aren’t currently on a PE routine (like me). I hope that shed some light on the subject for ya. For more, try doing a search for “injuries” “erectile dysfunction” or “discoloration” — there should be plenty to fill your noggin with what pops up.