Of course.
There isn't as much fluctuation from system to system as you seem to think. It does exist for some players, and yes there's more fluctuation than offensive stats, but for most players, the advanced systems do peg the players at roughly the same level. And from year to year? Yeah, offensive stats do that too...
The +/- system does judge every ball on it's path, how hard it was it, speed, etc. That data, plus the video analysts, is used.
FRAA is based off the basic stats - putouts, assists, errors, etc.
And here's an introduction to
UZR, from 2003. The system's been updated since.
I'm not really sure exactly what your point is. Is it to not look at the stats? We definitely should look at them. Is it to not trust them as much as we trust offensive stats? Yeah, of course. I'm just not sure what you're objecting to. It seems every time somebody mentions advanced defensive stats, you make it a point to post and say this same stuff you're saying now, if I recall correctly. I'm not sure why.