So after doing tons of reading and looking... The 97+ has a U-Joint at the steering wheel to column connection which runs just through the firewall and connects to the intermediate shaft. Given that the first U-Joint (at the steering wheel) is supported in 2 places by the frame of the truck under the dash and at the firewall, it basically eliminates its ability to cause 3-4 inches of travel causing any kind of bind. As long you support every third (in a line) u-joint, it doesn't mess with the geometry as it only allows one direction of movement (vertical or horizontal).
Your chassis and frame do not flex opposite each other nearly enough, unless jumping your truck, to produce a situation in which the shafts could bind from improper geometry.
However, Borgeson DOES NOT support the 97+ with said shaft. In theory, if you were to cut only the bare minimum from the shaft so that there is no COLLAPSE, during an accident, this could cause the driver harm. However, if you cut enough to allow for travel, you should be in the same boat as the OEM shaft. They are really the same principal minus the crappy rag joint. Again, it's at own risk, but I think that alignment guy was misinformed.
From reading problems with the Jeep intermediate shaft in swaps pre 97, the shaft collapses internally and lets your steering wheel move while not turning the gear box. I think that could definitely be a hazard, possibly what the alignment guy had heard of as well.
Just throwing it out there for everyone who stumbles across this!