So here are my findings thus far...

If your finding eggs "oocysts" and doing fecal floats the type of parasite needs to be determined. The specific type of parasite so that it may be treated accordingly. (for example... worms are treated different and with different medications then say coccidia oocysts... aka: coccidia eggs)

The article recommends doing a consistently measured and evaluated system where there is a formula involved to get a decent idea of the amount of infestation within the animal.
Personally, I will make efforts to treat my animals to alleviate them from carrying any parasites.
To say that they all carry these parasites and that carrying these parasites is part of their normal gutload is an over generalization and not substantiated by hard evidence and/or lab results.
The parasites lay eggs (oocysts) many animals normal immune system will keep these parasites they are harboring in check So an outbreak/attack will not occur. But they are still harboring the eggs or parasites themselves.
Furthermore...
this is not an innate feature from birth (natural gutload) but an external one from the environment to which they were exposed. Although these vermin are rife, common, easily attained as well as spread. They are not supposed to be in their systems.
When stressed the animal can have an elevated rise in parasite levels because their immune system has been compromised therefore the oocysts will sporulate hatch (quickly multiply essentially) and attack intestinal wall tissue in most cases. Such as what happens with the coccidia. Hence the excreted blood and wet runny stool.
The objective is to identify the parastic eggs and worms before this can be allowed to happen to eliminate the threat to the animal all together.
To just say... "a few coccidia is part of their normal gutload and that you know you will always find them etc etc."
This leads me to deduce that the person either 1: does not have a microscope and perform regular fecal examinations or 2: has mearly read up some basic forum knowledge and has not throughly engaged in the topic.
Need I say more?

Here is some literature from the article:

Evaluating the Results
How many eggs is too many and constitute an infestation? Most alpacas and llamas have worms, so, do not panic if you find worm eggs in the sample; that is normal. There is no shame if your animal has worms. A healthy animal can function quite well with a "normal" worm load. Its body can naturally digest and absorb its food and remain anemic-free. But when the animal undergoes stress and other health problems, it becomes susceptible to worm infestation. Large amounts of rain and warmth can also increase worms and parasites in the pasture. Unfortunately, worms and parasites may become resistant to worming medications.
The goal is not to have your animals be totally worm free, but just to maintain a consistent low worm load, with the animal showing no signs of parasite infestation. By this method, your animals will build a natural immunity to intestinal parasites.
You need to consult with you vet about recommendations for worm counts. In my area (East Texas), my vet recommends that 10 eggs per gram indicates that worming is required. If the count is lower than 10 eggs per gram, say 5 to 7 eggs, I resample in 2 weeks.
When you are treating your animals with chemical wormers, it is standard procedure to identify the exact type of worm eggs, so that you are properly treating with the correct chemical wormer. Different wormers kill different worms. Your vet can advise you about which wormer medications are appropriate.
NOTE: Be aware that you cannot always see signs of LUNGWORMS in a fecal sample, due to the fact that mature Lungworms reside in the lungs and not the digestive system. Your animal may have Lungworm, and it not show up in a fecal sample.