No contradiction. The innate system is important in that it allows the fish to survive long enough to develop its adaptive immunity. A fish with a great innate immunity will still be killed by Ich and Velvet if present in large enough numbers.
I still don't know what you think the innate system is doing "while we wait". Did you read Paul's fish slime thread? The entire innate system is rife with
lethal and inhibitory anti-pathogenic compounds.
Think of the innate system as a can of gasoline. Think of the adaptive system as a sniper.
The fish can use either against their targets. If you have him equipped with a gas can the size of a nursing bottle, then he'll get just about that much use out of it. (Even at that, most folks have poked a hole in the nursing bottle...easy to do better than this once we know how.)
Keeping with the analogy, Paul's fish don't mess with a nursing bottle, they drive around in a gas truck, thanks to the awesome feeding routines, and with a sniper turret on top which is fully armed thanks to his wild mud and sick fish.
I'd love to know how much action the sniper really gets. (I am pretty sure they are actually able to measure this in a lab nowadays....even at the aquaculture level I think.....know any fish doctors
@Paul B?)
Yes, this is why the system will not work without a competent innate immune system. However, it is still necessary to have another component to mitigate parasite levels until the adaptive system has time to adjust. In the ocean, currents are constantly washing away some amount of the parasites. In an aquarium, it takes something like ozone or a UV filter to replicate that effect.
I look at it like their adaptive immune system is slow because, like you said, they usually don't have to weather wave after wave of parasites...one wave, done. They, and the ocean, have both moved on. No need to call the army unless the assault persists for some time....and only then then is when the big gun comes out. It supposed to be rare, but it's still something they were built for.
(Not all, evenly though...amazingly, even differences in fish color (among many other things) can indicate some difference in their immune capability. I think I read that red fish have greater immune capability and blue have greater reproductive ability. Red is literally an extra store of carotenoids, which are fuel to the immune system. Blue literally attracts more mates. IIRC they were looking at Hippo tangs and Clownfish as their examples.)
I don't think this complicates the fact that the immune system works like it does
and needs to be supported. That's all we're saying here.
Why bother saying it? Lots of reasons....mostly all the same reasons I used when I was in retail. It's the info people need to have long term success with their fish.
Some wellness recommendations we read on here and elsewhere don't account for the immune system, or even outright deny its role. Putting an apparently healthy fish prophylactically into a 10 Gallon PVC-decorated QT for 3+ months with copper would be one stereotypic version of this recommendation which illustrates most of the bad points a recommendation can have. The only way to make it worse is to make the example fish a Tang.
Following these kinds of recommendations can reduce or even eliminate a healthy fish's whole immune system. (Forget about losing some specific immunity...least of its problems.)
Usually this recommendation is given to a newbie who has no idea....then even if the QT routine they've been assigned "works" they go on abusing the poor fish with (e.g.) flake food, bad roommates or cramped quarters, etc. Maybe all of the above. Without the fishkeeper having more information on what supports the immune system and what compromises it, the conclusion on those fish hasn't been changed by QT, just delayed a little.
Immunity has been proven to be effective with Crypto, Velvet, Black Ich, some bacterial infections and also some internal parasites. No reason to limit it just to Crypto.
I was only saying that Ich was the specific example we had been talking about up to now....the conversation was not incomplete or limited is all I meant.
And I don't think the general theme is limited. Paul's actions on his fish's behalf seem to work against everything.
(Which is a telling sign of gas can work more than sniper work!

)
And on one last note for Ich.
I'll say I'm surprised that we haven't heard of anyone on here tracking down an Ich vaccination for their prized fish. They supposedly exist (they're written about in the literature), just not in an economically viable form for fish farmers. That market wants it to cost pennies per dose and they need it in a form that can practically dose thousands or millions of fish at once.
We have no such requirements.
I think I could name six people in the hobby that, if they could, would spend $100 per fish to get their fish vaccinated vs Ich.