In the real numbers, which are not always simple or intuitive, 0.99... = 1. That's true and I seem to understand the proof.
But the real numbers aren't the only system that might be sitting behind "0.99..." and "1" when I write those symbols down and talk intuitively to people in my family. The reals are just the system we're taught first.
I believe there are other systems (I think the surreals are an example) that work just as well for everyday purposes, but where ( my understanding is that) there are numbers that differ from 1 by a value that approaches zero, yet those numbers are not equal to 1. (I've played with the surreals but only as a hobbyist.)
If you do calculus in these other numbers, I think physically meaningful problems will still yield the same answers. (For example Zeno's Paradoxes are still not an excuse for failure to attend school.) But it isn't a law of nature, I think, that all number systems that can hold 0.999... and 1 must make them equal.