If I played alot of open E string runs ... hammer-ons /pull offs and stuff ... E at concert pitch makes the most sense ... but since I don't and I have been tuning my Es flat for so long ... having them at concert pitch would throw me off.

Once you get used to your "open string JI set-up" your ear/brain will make all the necessary micro-adjustments with the bar automatically to "fit in" with the backup.