If the flanges aren't parallel, it will vibrate. A CV shaft isn't appropriate unless the pinion flange is pointed at the tcase flange.
Offset side to side, within operating limits of the joints on the shaft, does not matter so long as the flanges are parallel. No different than the vertical offset we are used to. Ujoints can't "tell" a difference.
With a Toyota axle, the fix would be to cut n turn the knuckes so that the pinion flange was either parallel to, or pointed towards the tcase flange and then run the appropriate style dshaft. I'm not familiar enough with Ton's to know what most do in this situation, with that axle.
I did not want to deal with the front driveshaft vibe issues on my 80 the "proper" way (cut n turn), so I installed a part time kit. Granted my vibration was only noticeable above 50mph. Extra oomph around town and less wear on front end were definate plus's.
I know a lot of 80 series guys see the CV shafts as a "fix-all" for driveshaft vibes, and they may help, but properly setting pinion angle is a LOT cheaper, not to mention no plates, bushings, or arms are necessary for correcting caster when a cut n turn is performed.