"of course tuning a guitar (fixed frets) using overtones (3:2 ratio on open strings) never sounds quite right for the fretted notes."

It CAN'T EVER!!!

Because unless the frets on your guitar were SPECIALLY cut to the EXACT correct places mathematically according to JUST intonation, your Luthier would have merely used the 'normal table of intervals' built for 'EVEN 1/12 TEMPERED' guitars!!!!!!!!!!!!!!!!!!!

You are trying to MIX TWO mathematically INCOMPATIBLE SYSTEMS OF INTONATION!

And btw, I will extremely surprised if the 'normal even tempered tables' did not also contain subtle 'modifications' for shifting the correct theoretical mathematical upper fret placings, to compensate for the practical effects of shortening the length of practical vibrating strings by stopping them on the frets (thus also slightly stretching the strings and changing their tension!), so that the instrument just (sorry!) 'sounds sweeter' at the higher frets!

Oh...

The word 'just' for that method of tuning/intonation came from the same greek word from which we get 'Justice' - and basically meant 'an even distribution' ... confused yet? ;-)