Brother...
It's hard to get kullu means part... Kullu can only mean all or each.. When added min kullu it can only mean from all or from each...
No, I think you are restricting the verse to one interpretation, while ignoring the others.
The verse did not say "kullu zamara" (all fruits), which Allah could've said simply, but he chose to be very specific and Allah added "min" to that verse to say "min kullu zamara".
That means: "of [all the fruits]" or "some of [all the fruits]". The word "min" can mean 'of', 'from', 'some of', 'some from'.
So when you say, some from the set of all the fruits, you are saying something that carries a connotation of high magnitude while at the same time not necessarily saying "every single one".
Imagine the set of [1,2,3,4,5,6,7,8,9] and I tell you "pick some of the numbers from all the set" or "pick numbers from the whole set"--that doesn't necessarily mean pick every single number. Likewise "min kullu zamara" does not mean "every single fruit", it means "of every fruit" or "some of every fruit" or "some of all the fruits".
In English, I can say "of all the fruits, some of them are sweet" or "of all the fruits, are sweet ones". The same in Arabic. Allah used the word "min kullu" and not just "kullu".
I went through min kullu verses it clearly indicate within the context of all or each...
First, I think you took the wrong approach because you are thinking we need verses from the Quran to reduce the ambiguity. Sometimes, the Quran may not explain some of its ambiguities...and we are left with those ambiguities. And we already know that "min kullu" can mean those 2 different things. If they can mean those things, then they can mean those things

That alone is sufficient.
Even the couple of example you furnished cabnot be taken as part of.. Context of the verse or intention and subject is key...
If I say I gave from all I have to you...it does mean all.. Not leaving anything apart but what is the subject... What did I give.. Money... Money is what I gave all not any other thing...
Sure, that Dhul Qarnayn verse is just one I picked randomly. I'm sure I can search for many, but why do such a thing after what I just explained above? Also why did you forget about Quran 39:27? This tells us specifically that "min Kullu" cannot always mean "every single one", but rather means "from the set of all ones". Again, Allah could have just said "we have given you "kullu" examples", but he didn't, he said "min kullu" indicating he only gave us examples from [the set of all examples].
But even then, the assumption that we need a Quranic verse to remove the ambiguity is non-sequitur. If something can be understood as X, Y or Z, then it can be understood as X, Y, or Z, even if the Quran did not specify which! Don't fall for this trap.
Even 3:07 is talking Bout a particular word.. But it talks about verses (aya) so what you connect is not so adhering... Here only a word or two.. That also clear Arabic words kullu and min..
No, it's far more complicated than that! There could be ambiguities within large verses. Some verses are super large and they have phrases in them that are ambiguous.
If I say "there are medical conditions which present with mild pain and others with severe pain", I am not excluding the fact there are medical conditions with moderate pain nor am I excluding medical conditions with alternating bouts of mild and severe pain. Such an exclusion is not stated in that statement--its only the
presumption of the reader that leads them to that conclusion. Likewise, if I tell you there are sentences in this article with big words and others with small words--that doesn't exclude sentences with both big words and small words. Likewise, if a professor tells you that in your essay there are sentences that are well written and others, poorly written--it doesn't mean there aren't sentences with both well written and poorly written components. Again, such an exclusion is only perceived through the
assumption of the reader. So again, this verse (3:7) does not exclude the existence of verses which have both ambiguous and unambiguous elements within it.
From:
http://www.answeringislamicskeptics.com/approach-to-quran-understanding.html In my understanding 13:3 could mean that God created all zamara.. Then ja'ala made all of them genders Zawjain (genders male female).. I mean each zamara is both male and female.. Out of it two..
That's not what the verse said. Word for word here is what it said:
وَمِنْ كُلِّ الثَّمَرَاتِ جَعَلَ فِيهَا زَوْجَيْنِ اثْنَيْنِ
"From All The Fruits, He Made
inside it two mates"
So inside the fruits are two mates. The fruits themselves are not two mates, but inside them are two mates. That is literally what this verse is saying. And we find out that indeed there are double matings inside the fruits (and these are in their seeds!).
And note, because "min" also means "some of", that verse above can be rendered word-for-word: "some of all the fruits, he made inside it two mates".
I don't how logical with science but that's what I get from the verse.. Science can change but verse won't..
If a verse is worded in such a very specific weird way that happens to true to the science--that is VERY significant. The verse above is worded very carefully, and this carefulness and specificity is a sign for us.
Why didn't Allah say "fruits are created in pairs, male and female"? That would be a scientific error--there is no such thing as a male or female strawberry. But Allah avoided saying that and instead said "INSIDE" them, there is a double pairing. This specificity and carefulness of the Quran is very telling as to who the author of the Quran is.
I do understand that science is changing, but this is not just science, it is an
observation. With respect to double fertilization, that is not something like cosmology or social science where there is a lot of guessing, modeling, experimenting and rudimentary analysis, this is not an experiment, it is an observation--you can literally see it under a microscope! You can literally observe it. It's not really science, it's just observation at this point. It's kind of like observing the heart pumping blood, sure it is a science, but it's really more of an observation.
So in the case of Zamarath quantity is two but when it comes to animal qty is 4..
That's my take..
That is an inconsistent translation. It seems that you've just chosen to use the same exact phrase in different ways without justification.