Well, as you know, the scientific method isn't without its (kinda hidden) philosophical presuppositions which, if investigated deeply enough, invite their own problems.
Yes. If that was what he wanted to say I am wondering why he didn´t stop after the first 17 words (which got me intrigued), and immediately threw in all the rest of the stuff (which made me grouchy).
As for your last sentence, that goes with pretty much everything if you push it far enough, whether substantiation (even if you accept things under a scientific rubric, you're still assuming the philosophical presuppositions for science, a bit of a leap), explanation or elaboration (we can technically always explain things further, and determining whether something is explained or elaborated "just enough" is intuitive at best, definitely not the result of a clear external standard).
Yes, but saying "I believe that" and leaving it as that is not even an attempt of doing any of that.
Eh, maybe (great point). I see it more as saying that science is used to "transport" irrational ideas under the guise of science, and/or GIGO.
Ok. Since the criticism in the first sentence is directed at the fact that the scientific method itself rests on unsupported asssumptions and premises, it goes without saying that the results will never go beyond the boundaries determined by those premises. IOW, if the premises are garbage, the results have no leg to stand on. That´s a systemic problem (in case that the system is claiming to produce "truth").
But again: He didn´t leave it at that. He went on to say that "academic inquiry is, deep down, merely the elaborate justification of desire, bias, whim, and glory" - i.e. he stopped his systemic criticism and started to tackle the way this system is used and insinuated sinister motives on part of the scientists. Which are entirely different points.
Let´s just replace "science" by "mathematics":
Saying mathematics is a closed formal system (and therefore can´t explain anything beyond the defined boundaries of mathematics) is one thing.
Saying that mathematic inquiries are, deep down merely the elaborate justification of desire, bias, whim and glory would be a completely different, even unrelated one.
I don't think that's having their cake and eating it. More like defining an incredibly difficult metaphysical concept via negative reasoning (what something isn't), along the lines of: "God can't be physical, because something physical has X properties associated with the universe; therefore God must be 'beyond' the physical." Analogously to the whole *experience* involved in phenomenology: i.e., our experience of something is fundamentally different than (albeit possibly reducible to) any physical mechanisms in the brain. And trying to talk about the experience of something using concepts is no good, because the two are incommensurate with one another (one being ideas, the other being the experience "underlying" ideas and sensations, etc.).
How´s that any different than saying that the existence of the god of this concept isn´t subject to science, and therefore neither provable or disprovable with its methods? Just like you won´t be able to do it by means of mathematics or dentistry?
And I am not aware that anywhere in modern scientific research (nor in mathematical works or dentistry) the existence of such Gods have even been the subject - what exactly is the complaint?
God is defined as a metaphysical entity, therefore God doesn´t show up in science.
I am just not seeing how and why a researcher of, say, gravitational issues could possibly throw in God into his works (other than possibly ending each paragraph with "In God we trust", in order to appease theists, who find the fact disappointing that no God is needed to explain gravitation

). I am also not seeing how that allows for ascribing "desire, bias, whim, and glory" as being at the core of his efforts.
As for meta-scientific claims, you're always going to have those when you do anything but science.
Of course. However, I didn´t say there was anything wrong with meta-scientific claims. I just pointed out that those claims you brought up as scientific claims are actually meta-scientific claims.
I´m off to a 10 weeks Turkey vacation, hopefully losing a bit of the grouchy attitude.
Enjoy this, for a farewell:
Bright Eyes Land Locked Blues - YouTube
[FONT="]"I keep drinking the ink from my pen
And I'm balancing history books up on my head
But it all boils down to one quotable phrase
If you love something, give it away
...
[/FONT]
[FONT="][FONT="]You'll be free child once you have died
From the shackles of language and measurable time
And then we can trade places, play musical graves
Till then walk away, walk away"
(It´s not me, of course - I wish it were.)[/FONT]
[/FONT]