I was always under the impression that u-joints "vibrated" and by putting them out of phase from each other the "vibrations" canceled each other out. So putting it in phase would cause more vibrations.
Correct. They vibrate in rotation: they accelerate and decelerate as they rotate. If you have a U-joint in your socket set it's easy to see this. Snap two extensions to each side of a U-joint, and spin one end. When the joint is straight, the output shaft will spin smoothly. As you flex the joint while spinning, the output shaft will spin more erratically, it's accelerating and decelerating twice per rotation.
If you add another U-joint and extension, you simulate our driveshafts. If the second U-joint is 90-degrees out of phase with the first, it will accelerate when the first U-joint decelerates, and decelerate when the first U-joint accelerates. So it cancels out the accelerating and decelerating, and the third shaft (diff) will turn smoothly. If it's in phase, it'll further accelerate and decelerate the third shaft. Driveshaft U-joints should always be 90-degrees out of phase, but that can take some complex geometry.
For the joints to perfectly cancel, the two joints have to have the same angle (bend). If the input (t-case) and output (diff) are both horizontal, and directly in line along the truck, the joints will always have the same bend as the suspension travels up and down. That's how our rear driveshafts work. The rear suspension hinges on long arms to keep the rear diff fairly horizontal. You'll notice the three shafts (in the t-case, driveshaft, and in the rear diff) are in the same vertical plane, they don't bend to the side like the front driveshaft.
The front driveshaft is more complicated: the three shafts aren't all in one plane. They don't have to be for this to work, but the joints have to be rotated so they bend at the correct phases to cancel each other. At stock height and normally loaded, they are correct. With the suspension stretched or compressed off-road they aren't correct, but there won't be vibrations at the low speeds encountered off-road. A lifted 80 might experience vibration because the front U-joints no longer cancel each other on the road, you might need to experiment or take some measurements to get that right.
Continuous velocity (CV) joints don't have yokes, and don't have this problem. They're more complicated, more expensive, harder to maintain, heavier, and less efficient, but take up less space than pairs of U-joints. Birfields are CV joints.
