Great write up!
There is is "some" play in the driveshaft slip yoke into the the transmission. With a lift where the rear axle has moved down through a vertical plane then the trans to diff distance has actually increased and the yoke is not as far in to the trans as pre lift. By repositioning (using the offset plate) the entire axle forward then yes the distance will be shorter and the yoke will sit into the trans a bit deeper.
You can test the limits by disconnecting your driveshaft from the diff and determine how much range of slip in and out is available. Keep in mind that as the axle moves straight up through its compression this distance will get shorter. Conversely when the axle sags the distance gets longer. The slip range at the trans needs to accommodate this variation without fully disengaging and falling out of the trans or compressing so much that the yoke bottoms out and something is stressed or breaks.
Beastie 3: 2002 7.3 EB Cargo: Agile TTB, CCV Mid Top, Custom Walk Through, Lots of stuff added. BlingMyRig.com