Your question is very simply answered:
If you take any common, idiomatic, stock phrase, and then modify it, it sounds awkward.
That's the only reason "1" sounds awkward.
Issues of "logic", "double-negatives" etc, are all totally, completely, irrelevant.
A simple observation is that there are any number of very common phrases in - say - Indian English, which are common and normal there, but have the exact "jarring - is that a double negative or what?" quality you alludea to in "1".
Even more simply, the oddball formulations (which we're now familiar with and "sound right") simply once weren't, and others will be in the future.
It's entirely, totally plausible that your "won't take at least" formulation will be trendy in 5 years and completely normal in 50 years.
(Because English is the planet's absurdly flexible, loose, ruleless, morphing language, bizarrely your "won't take at least" formulation is starting to sound natural to me, minute by minute, literally as we discuss it here!)
[ Be alert to the critical point made by @rackandboneman ]
Steve: "It'll take at least 15 minutes to walk there." Bill: "Bullshit, it won't take at least 15 minutes to walk there, man ..."
Your "1" would have been used many times, in that scenario.
Summary. All you're hearing is the jarring effect of a common formulation or idiom being modified. That's all it is. "Logic" etc is completely unrelated here.
Your "1" is no more or less "logical" than formulations which do ("happen to") exist here and now.
It's an interesting observation that: there are many, many questions on this site (interesting questions) which are about the logicality of an issue in English. (These can range from spelling issues, to idiom-related issue like this one, to grammar issues.) The answer is always the same: logic is irrelevant in English.
I've coined a name for your formulation!
We've all heard of double-negatives.
Regarding your formulation,
It won't take at least 15 minutes to walk there.
I have named that a rebuttal-negative.
Using the spectacular observation by @rackandboneman, we know that (today, as of writing), rebuttal-negatives are only used in the unusual situation of a rebuttal to a long-group-idiom. They only (today, as of writing) sound sensible as a rebuttal (by adding the testy word "won't") where you're parodying the other speaker's a long-group-idiom. As in
Steve: "It'll take at least 15 minutes to walk there." Bill: "Bullshit, it won't take at least 15 minutes to walk there
, man, you're full of crap ..."
However! Rebuttal-negatives immediately appeal to me as a speaker. I'm going to start using them even before the other person gives the original idiom which I'm gonna parody.
So it's sort of a naked rebuttal-parody-negative.
I can imagine using this! Someone says ...
Man, it's gonna take ages to walk there, we need a taxi, my legs hurt ...
I then parody the abstract phrase take at least 15 minutes to walk there
as if some loser had said the abstract phrase ...
You pansy ass, what's wrong with your feet! It won't (seething parody of something not actually said) take at least 15 minutes to walk there
, what are you saying! Let's do it! Get walking!
You see?
You've invented rebuttal-negatives, bravo. They're kind of a naked rebuttal/parody of an idiom expected in the situation.
(Maybe this exists already, perhaps in stand-up comedy - I don't know.)