Debian uses the Schulze method (if things haven't changed recently), so I do not see how that would have an impact on the result.
The issues arises from how the 3:1 ratio is calculated. Which is by comparing the number of “change it” votes to the number of the “None of the above (NOTA)” votes (this is my understanding of from the email thread).
As a result the number of NOTA directly impacts the number to approval votes needed to win, as a simple majority isn’t enough. Thus having a NOTA option, and an option that looks like a NOTA can create confusion which splits the NOTA vote, because voting “keep public vote” above NOTA, which reduces the number of counted NOTA votes, and increases the number of “change it” votes (as all non-NOTA votes are considered “change it” votes, regardless of practical impact, at least that my understanding from the thread). Thus reduces number of approval votes need to achieve the super majority.
As this vote was won by a single vote, voter confusion on how choice ordering regarding the NOTA option could have swung vote against the intentions of the voting members.
In normal elections we see this with people who don't like any choice, but don't want to spoil their ballot. So they pick their next best favorite.
This means that if A is removed, people might pick B or C instead just because A isn't there.
People are tricky. Hard to pin down what's exactly going to happen every time. There are distinguishable patterns and such; but ultimately you can't rely on them as if they are infallible.
Of course people might not necessarily act rationally but you've got to draw a line somewhere, otherwise elections are simply undefined behaviour and talking about properties of elections becomes meaningless.
But, no, you cannot safely recalculate that result, because by and large people are the representation of chaos. undefined behavior is the norm, not defined behavior. Defined behavior is only present in any of our societies because of 'social norms', which is the only reason I relent and say that some assumptions might be possible. But I will not agree that you can 'safely' recalculate that result just using whatever assumptions some person arbitrarily has deemed 'good enough to trust'.
That kind of thinking is why most polls are actually wrong, but taken as good enough. (Yes, I'm one of those people who nit picks the randomness of their selection biases.)
P.S.
All it takes to swing an election in favor of the underdog is a single new revelation. All it takes is for people to suddenly question their previous choices. A & B might be their norm; but people can be swayed to choose C or D if the situation is right.
This is why we can't really trust assumptions without some sort of evidence to back them. At which point they stop being assumptions...
Otherwise you're just arguing the vote is invalid because it would have ended differently in a rerun, and you have to stop somewhere.
If you remove A as a choice, or B, people might go with their next preferred option instead of just not voting at all, etc.
This means you can't know for sure that results would equal the same with or without that option, because you cannot actually assume all actors will vote the same every time. To even begin to think such a thing as true is just asinine when the world proves to us on a daily basis that people are willing to compromise on their beliefs all the time. (No offense.)
For those that are wondering (like I was);
Google & Wikipedia:
"The Schulze method selects a single winner using votes that express preferences. The method can also be used to create a sorted list of winners. Therefore, if several positions are available, the method can be used for this purpose without modification, by letting the k top-ranked candidates win the k available seats."