capo always out of tune

okay. i’ve been playing guitar way too long to not know this... but here i am

i tune without, then try to muck around till it doesn’t sound complete flat with the capo. then i’ll pull the strings to make sure there is no give and the capo is on tight and fretting like it should.

however notes are generally not in tune. i’ve been told that tuning again after setting the capo can mess up the intonation. but is that only if the capo is left on long periods? is this just to avoid tuning multiple times, like after the capo again?

what’s the real way to get a capo on the neck without all my notes being out of tune. i generally give up when it sounds to be in tune with itself. albeit those are a bit flat on the clip on tuner.