Even if you don't agree with his general points about int as a longevity stat/spirit as a throughput stat (via changing your spell selection, in opposite directions), I think we should all be able to agree that spirit flasks and food give too little spirit for the "slot" they take up, except maybe a few specialized mechanics like MTT.
For the most part yes, barring certain things like a healer being undergeared or at the very least not having a good amount of spirit for the encounter along with certain mechanics of the encounter itself. It's a rarity that I've ever used a spirit flask and almost always use intel flasks and food for my healers. But again that also has to do with the classes I play. If I ever really did get into Holy I don't know if I would go with spirit flasks/food in that spec.
There was just something that put me off about the whole article and I've had difficulty putting my finger on it. It's almost feels like he's missing the very point he's trying to make. Yes, if you're having issues healing that stacking more spirit isn't going to make you a better healer, but at the same time it feels like he's ignoring a whole bunch of other factors. That's one of the problems I've had with it, along with seeming to assume that all healing classes would value the same stats. I'm not talking about what was discussed in the comment section but the main body of his article. He doesn't take into consideration Rapture and MTT for example and if one was going to talk about balancing spirit around your other secondaries and intel then you either need to address all of them or only talk about the class(es) you know.
I think the part where he equated a spirit flask during a three minute fight as giving you the ability to cast two rejuv's rubbed me the wrong way. It's not the break down of how much you're actually getting back over three minutes, I think it was how he was so flippant about it as if there were no other factors at play. I think he just made the whole thing at least sound terribly over simplified, which was evident in the debates that followed in the comment section.
-Risk Mitigation - It's a frequently used argument that you should gear around ending fights at 0 mana, and any more than that means you are wasting itemization on Spirit. The issue with that argument is, you are assuming fights always go the same/always go perfectly. If something goes wrong, forcing more mana to be spent than normal, gearing around ending the fight at 0 mana can easily become "OOM with 3 minutes left". If you have sufficient throughput to get through the fight, there is some benefit in having extra regen so that you can push harder/last longer when things go sideways. After all, preventing wipes/deaths is the primary role of a healer.
I've heard this more times then I care to count being told to healers. I used to tank a lot, long before I ever really got into healing and listened to healers being told this.
To me, if the raid perfectly executes the fight then I should have mana left. As you said, not having a buffer will cause your raid to suffer if anything goes wrong (and sometimes things just go wrong due to bad timing and RNG) and could potentially limit your ability to recover and keep the attempt going. That's really a terrible way to look at things and limits you from being able to do your job effectively, especially in progression raiding where errors are part of the learning process.