I can't really answer that on any technical level, but it just doesn't seem to be a problem for me at this point. Early on, when I first started doing this, and had to really work at relaxing my lower back (due to the back injuries), I would definitely feel that my lower back was being strained (not in a bad way, more like worked hard) when I would consciously relax my lower back/spine and do things. That fatigue seems to have passed and I guess that my body has just adjusted and gotten stronger. I would think at this point if it were going to impact my spine in a negative way, I'd be feeling it by now, but the exact opposite has been the case. My lower back feels better and stronger now than it has at any point in the last 15-20 years.
My guess, and this is only a guess, is that it has a similar effect as focused lower back stretching, inversion, etc, in that it allows increased blood flow into that area of my back, which helps. I also think that the compaction gets regulated by the body as you get better at relaxing those big muscles and letting the less prominent muscles get stronger and handle the load. It probably wouldn't be good to just jump in and try relaxing your lower back with a big load on your shoulders, but much like any sort of weight training, you build up and increase and get stronger as a result.
Funnily enough I had a recent reoccurrence of back pain inherited from 20 years ago, basically a spinal Protusion in the lower lumbar. As it gets more and more painful I find myself doing less and less ukemi. And classes have now gone down to twice a week. It's not getting better, and I'd be kidding I didn't think it's getting worst.
Confounding myself trying to figure out what's wrong I decided to restart gym work which I abandon upon advise of my Sensei and Silat teacher. Well two days on the elliptical and weights have resulted in diminished pain. Thus I agree that the exercise and loading of weights does strengthen the body.
Now... Wouldn't it be a surprise that all the exercises you guys are doing in developing fascia, grounding etc... Really was as simple as making your body used to taking lateral loads rather then generic strength training. And that's all it takes for people to do amazing stuff with their bodies. Specialize muscular training and unified usage of those muscles.