Luckily, for all intends and purposes we so far, and in the foreseeable future, and probably forever, have to consider, infinitely close is just as good as being identical. So I see no reason why we would have to take it away from what you call "real analysis" (and which I would call "useful analysis" if we have to call it in such judging manner) and which, also, with much ease explains why the assumption that 0.999... = 1 works just as well weather it is true or not.
So the problem you see seems to be without any of the consequences you imply and hence not like a problem.
As much as I employ the "eh, close enough" approach myself, this is a dangerous thing to do. If you take out central elements of real analysis (a technical term with no judgement intended by me), it is unclear what happens. A lot that is based on that might come tumbling down. If something is just infinitely close instead of exact and then you go and do this an infinite amount of times, the result is totally undefined (the what is infinity times 0 problem).
Or it might work and you end up with some sort of para-analysis that has different axioms, but ends up with the same usefulness. Who knows? If people want to try to construct something like this, I have no qualms with that. But they should come back, when they have shown that there is a consistent system instead of making vague statements based on pseudo-math.
Regarding "whether it is true or not": What kind of truth are we talking about here? Within he axioms of standard math it is undoubtedly true. Within some kind of para-math it might not be true. So what do you think is the standard here?
So I am unclear what you think the implications of "as good as science can prove such things" are, considering that my objection towards the idea of a finite nature of physics regarding its downward scale are entirely based on the limits of what science can prove in that area.
And now you seem to agree with my original statement.

But in the beginning, you told me "Yes", as in yes, I can prove to you that this is not just an impression due to measurement limitations.
edit: But I agree this is irrelevant to the actual question. Which from my POV is weather 1=0.999... violates the rules actual quantities operate on (rather than the rules of the tautology called academic mathematics)
Let me rephrase that: In science there is no absolute proof, but the wiggle room can become extremely (not infinitely, I would guess...) small. To that standard, we have proof that there are fundamental limits to our knowledge of quantities, independent of the measurement device. That fundamental limit to our knowledge could also be a fundamental limit to reality itself. Whether it is, is a matter of debate, but in my opinion, the evidence is strongly in favor of that.
There needs to be a kind of abstraction that is grounded in reality and one that is not.
For instance, I'd argue that the rules of a sport are not grounded in reality. They are probably best understood as a matter of pure will. They are not dictated by an a priory existing fact of life.
Do I have a say over the pieces of an apple I see?
Are quantities more abstract than physics?
The reality of the instances of sth and what this actually means. Math is supposed to articulate that, as you yourself said. I am saying that while academic math does a fine job in usefully articulating it, it not always entirely correctly articulates it. Whereas in the case we discuss this incorrectness is virtually non-existent. But only virtually.
I agree that there are abstractions that cannot be described as grounded in reality. That does not answer what an abstraction grounded in reality is supposed to be. You do have a say over the pieces of apple you see: You could see them as a collection of very tiny apple pieces on a molecular level. You could see it as a fraction of one whole apple. Or you could see it as a fraction of an apple tree, or apple carton in a store. Even if we constrain ourselves to separate pieces of apple, what counts as separate? If two pieces slightly stick to each other, are they still two pieces?
There are abstractions that are useful to describe reality. But of course, these abstractions are never a perfect image of reality. Therefore I do not think it makes any sense to say anything about the truthfulness of abstractions. Certainly not by comparing them with reality, as this would be a test that every one of them fails. The only thing one can say, is whether abstractions are internally consistent.