Maybe I can clear this up (please note that my information will be biased towards the KZ products due to my profile):
1. Probiotic systems assume that you have stable water parameters in place. These values must reflect NSW levels, not the elevated levels that are typical of artificial reef systems. Of these, the KH is of particular concern. Do not elevate this value beyond 8.0.
You will also have to start paying attention to the potassium levels since the Redfield ratio starts to matter once the bacterial colonies start to manifest.
2. The warnings assume users have done zero research into the topic and/or are not following directions. Granted, any product, if misused, can cause catastrophe (heaters, uncovered MH bulbs anyone?).
There is also wiggle room regarding the dynamic nature of every reef system; e.g. you can set up two identical systems (water volume, rock volume, livestock, equipment, etc) and come back in six months with wild variance on either.
Either way, it's expected. Ever read the warning labels on a paper shredder? You should see the documents on the commercial unit I have in my office.
3. Many of the additives can be used within or without their probiotic components. However, many of the supplements only produce optimized results within the context of ULNS. How you get there is of little concern.
4.
Not quite. Skimmers and chemical medias are passive filtration methods that rely on organics and nutrients being delivered to them. You can't, for example, break down a nutrient deposit within your rockwork or sandbed by using more GFO. It will continue to remain sequestered within the substrate until agitated into the water column.
Probiotic systems route this by developing a microbial community that can integrate into the biological stratum of the entire system, depleting nutrient batteries and making them unavailable to more obtrusive lifeforms. Eventually, these biomass's and their mineralized nutrient loads become exported by mechanical means (skimmer, water changes) as they enter the water column. This is possible since a large part of the manifold strains are bacterialplanktonic.
Anyway, if you want a scientific insight into this topic (with empirical data and research documents), go here:
http://zeovit.com/forums/forumdisplay.php?f=76
Gary (mesocosm) has assembled a veritable library of information relevant to this topic and has paraphrased much of the research jargon into laymen terms (or close enough).
HTH