In my last post I've stated that something like this, according to some experiments, perhaps doesn't work.
I was wrong
I've made an error when recalculating some resulting offsets, but after fixing that stuff, everything runs fine. So it's definitely not necessary for the sections to stay in sequential order inside the file.
Although it may be an interesting thing, it's kind of pointless. As you've reminded me a few posts above, the goal should be to completely delete the unnecessary sections, not simply shifting them around. And if the point would be just to reduce filesize, it's enough to set the raw size of sections containing only zeros to zero.
I suspect that after wading through knee-deep hex-editing stuff I've reached the same point where I had started
So it's time to rethink the matter!

Regards
Wurstgote