When setting this guitar up I did all the right things measured from nut on neck to 12th fret and from 12th fret to where middle of saddle positions should be.
FWIW, when setting the bridge position, you're better off measuring the full scale length from the nut rather than 1/2 x 2. The 12th fret can be out by up to 1mmą and the strings will still intonate fine providing the bridge position is correct.

That said, guitar building is not (always) an exact science. I have had the bass E intonate as far back as 654mm on strats.
Even different string brands (or batches) can intonate in different places. Weird and inexplicable things can happen with this stuff.