My first guitar teacher told me that someday I'd start to notice that you can't get all strings perfectly in tune. At that point, he said, you'll know you're getting somewhere on the guitar.
That’s an issue with tuning instruments in general, and why pianos are generally slightly out of tune as a compromise.
As you get used to a particular guitar and strings, as you train your ear, you can also learn to work around the imperfections by adjusting how you hold down the strings (even with a fretted guitar, you can slightly repitch a string by holding it differently).
Been thinking of going a bit lighter recently, and also getting a classical.
Doesn't help that most tuners are still dog slow, none of the beginners courses properly tell you how the guitar actually works, or what a "chord" really is. They're all just "play this and don't worry about it". To be fair it does get you going.