It's not unusual for the action to change somewhat over time, especially with newer guitars. It has probably gotten a little higher since its last setup. If you've never had any fret work, and you play daily, then look no further as to the cause of your intonation problems. It's time for a fret dress or a partial refret.
If you care about being in tune, then string stretching is absolutely necessary. Folks who say it ruins the strings are doing it wrong. If you just gently pull the slack out of the strings until their pitch stabilizes, then no harm will come to your strings. FWIW round core (DR) strings are awful and should be avoided.
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