Tuners are precise...so they offer no forgiveness nor do they account for the natural "personality" of every instrument. IOW, not every perfectly tuned guitar will sound equally "sweet" when you play chords.
Tuning by ear is OK, and then going from string to string....though any small imperfections end up getting carried over from string to string, and possibly compounded. So when you have to record a variety of instruments & voices...having a single reference is IMO the ideal way to go, and that's what a tuner does for you.
What I do is tune each string with a virtual strobe tuner, but then I'll play some chords at a few points and make some minor adjustments so the tuning not only measures up to the strobe tuner, but it also fits the specific guitar I am using.
The other thing....if you use a precise tuner to set your intonation, you are more likely to have sweet sounding chords when also tuning with the tuner.
Anyway...whatever method you use, if the tuning ends up working for you, and you can play along with other instruments and everything sounds sweet....then stick with your method.
I have to say, I've heard far to many mixes around here where guitars are clearly out of tune...and the person never noticed it, so I'm starting to believe that some people are just less sensitive to out-of-tune stuff, and they don't notice minor pitch issues.
Sounds like you have sensitive ears.
Not to mention....if you use A=440Hz, then your guitars will sound that much more out-of-tune than if you use some other reference.