ves said
If I tune my A to 440 and play double open strings and listen, eliminating 'flutter' or dissonance (in other words, playing perfect fifths), the D and G I believe will be sharper than that in equal temperament while the E will be flatter.

No, the opposite is true. 

Under either Just or Pythagorean tuning, the pitches in a fifth are in the ratio 3:2, that is, exactly 1.5.  Under equal temperament, they are in the ratio of the twelfth root of two raised to the seventh power, approximately 1.4983071.  So a Just or Pythagorean fifth is a little bigger than an equal fifth.

That means that under Just or Pythagorean tuning, the D and G strings will be tuned farther from A, therefore flatter, and the E string will be tuned farther from A and sharper, than under equal temperament.

When A strings are tuned the same, the G string will be about 4 cents flatter, the D string 2 cents flatter, and the E string 2 cents sharper than under equal temperament.

Electronic tuners are usually set up for equal temperament, but it's a matter of software to set them up for Just or Pythagorean tuning.