Mark, your question is smart, and you are totally right, there seems to be a sort of strange tendency, or disconnect, or misplaced cavalier attitude, among far too many bpl backpackers to disregard toxins or to discount them, so your posting is a welcome one. For example, cooking in a bpa lined beer can... shudder. Certain people here I do understand why they tend to do this, it's the simple old formula of not questioning too much or rigorously the source of your income...
Of course these things are toxic, reading the msds for any fuel shows all kinds of nasties, and they don't really even have to be honest about what they actually say is in there, at least not judging from the ones I've read where the proportions listed are mathematically impossible to achieve, ie, they don't add up to 100% no matter how you combine their numbers. And certainly most people commenting about the stuff being safe have probably exactly zero idea of what happens to say ketones when the methanol/ethanol evaporates, or if trace amounts routinely enter your body, I certainly don't know, but I'm sure it's not good. And remember, the word 'denatured' is just a polite term for 'toxically poisonous so you cannot use it to drink'.
I've been starting to wonder the same thing recently as you, primarily because I've been doing so much stove testing, where you really start to notice the toxicity of the substances (please people, do NOT test these things indoors), I think the thing that triggered my increased awareness was talking to a real chemistry professor, who noted that in the labs, they are not allowed to even open methanol unless it's directly under a ventilator. That's open, not burn. SLX is half methanol, give or take some unknown percent.
I don't think putting the stove in a plastic bag is foolish, but I do suspect that rinsing the pot out with water should be enough in general re dilution and removal of toxins, as suggested above. And the question of leaks of the smaller fuel bottles, if stored in the pot, is also a very good one, that I think I'm going to reconsider, while I like having it in there, I don't like ingesting toxins when my goal is actually to be in nature, some parts of home really are best left at home.
Nice to see someone thinking about stuff and questioning some basic bad practices that we tend to not think about just because they might be 'convenient', or let you get on the trail 13 seconds sooner, or whatever.
Also re burning the fuel, unless you are achieving 100% efficiency, ie, burning fully all the alcohol, you are almost certainly getting either non combusted or partially combusted vapors, and the partially combusted ones do some interesting things in terms of what chemicals they turn into on their way to the full combustion by products you see listed on the chemical pages on say wikipedia, you know, co2, co, water, etc, but that's only in a theoretical perfect combustion, that's not what the actual exhaust vapor contains, as one interesting discussion of this I think on zenstoves noted, actually nobody knows fully what chemicals are produced in the flames until it's fully combusted, it's a range, interesting reading by the way.
Pure ethanol is the only alcohol fuel where you can totally ignore all these issues, it's safe, except for drinking too much, of course.