I agree with many here that pure methanol and ethanol in and of themselves are not that toxic unless relatively large amounts are ingested directly.
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Lab workers regularly use them CLEANING AGENTS in lab environments and compared to the other TRULY toxic stuff they handle, the various pure alcohols are not much of a big deal.
The problem as I see it for a backpacker storing stove fuel and components is three fold.
1) In storing stoves, some stoves are made with components that have resins ,pigments and other nasty components on them and when they burn and char the residue on them is not something I would want inside my cookware, especially if cooking for others.
2) The various denatured alcohol blends (even the "green" ones ),ARE denatured, which is a polite marketing term for POISONED. The denaturants (Tolueenes etc) are pretty nasty.. Again, not something I would want in my cookware if I could avoid it.
3) Practical space considerations..Unless you are carrying REALLY small bottles of fuel, most of them will not fit in a cookpot anyway. Certainly none of the 4 and 8 oz bottles will.
My system is to take a 4 oz or larger round plastic fuel bottle and wrap my windscreen and stove floor around it. I cover that with a peice of Tyvek withba rubber band around it to prevent any snagging . If I am stowing that inside my pack , I usually put that in a ziplock in case of any leaks. If it is stowed in an outside pocket, I migbt skip the Ziplock.
To me, the inside of a cookpot is better used as space to stow cups, bowls and eating utensils etc. At most, the only stove components I put in my pot are my lighter and my stove burner in a ziplock. Many times they will go in the Ziplock with the fuel bottle ,if the burner is stoutly made or slips over the fuel bottle.
So it basically still only breaks down into two basic peices in my pack. My fuel bottle /windscreen assembly and my cookpot.. No "bits" floating around ..