There's two things going on here.
As a pilot, I'm familiar with hypoxia and how it works. I or pretty much any other pilot could very quickly write a completely bulletproof execution protocol that would guarantee a 100% painless death every time. It would involve a non-rebreathing 100% nitrogen mask so every lungful taken is 100% fresh nitrogen. In this mode, you just get drowsy and euphoric and pass out with no physical pain.

If they ask me to write it, I don't care if they offer a million dollars I wouldn't do it. I think the death penalty is barbaric and the way we have applied it is even worse, given how there are numerous instances of people executed despite evidence they were innocent being blocked by court procedure and prosecutors. I'm not saying there aren't people the world is better off without, there absolutely are. But if we are going to kill people, we need to be absolutely 100% totally fucking sure beyond any doubt regardless of procedure. So I will not support the death penalty.

And that brings us to the two issues.
First is that very few people who actually understand how to do it have any interest in writing good execution protocol. Thus a lot of the protocols are written by people without understanding of human physiology. And quite frankly, I would rather that be the case, if only so it is easier to challenge capital punishment.

Second, is that I think some of the people who write these protocols actually want to cause suffering. I say I'm a pilot so I have understanding of hypoxia, but none of my knowledge is unique or difficult to obtain. A quick Google for 'painless death nitrogen' would tell you everything you need to know.
So when I hear that the condemned is breathing his own CO2 from a bag, I conclude that either whoever wrote the protocol doesn't have Google, or they are intentionally writing a protocol that will look good on paper but cause suffering in reality. Or the protocol is being implemented in such a way to cause suffering, for example if the nitrogen flow is not enough. An executioner could easily prolong suffering by simply using less nitrogen, causing the prisoner to breathe CO2 and thus feel panic reaction.

But I think that further illustrates why the death penalty is a bad idea. The fact that the entire stack from prison guard up to Governor isn't 100% focused on a humane death sense to me we need to clean our own house before we start burning others.