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.