When you say flex plate do you mean the rubber piece at each end of the shaft? (guibo)
These driveshafts only have one proper orientation, each end is 180 degrees opposite of each other (in phase). However it would make sense that the diff and trans flanges could have high or low spots hence the need to rotate them to find the "right spot" if they are not marked during removal.
This would also ring true if one was to replace the original driveshaft with a used one and a vibration occurs.
Thank you for sharing your experience as there is very little knowledge outside of the repair manual on these specific driveshafts.
