As a rule, shocks that will work properly w/o needing bumpstop extensions can compress short enough to allow compression to the same point as a stock rig....in the case of a gen 1 Xterra, that's 16" or less as being fine.
Once a shock is found that compresses short enough, it next just has to extend long enough to allow full droop....which the OEM ones DID NOT DO.
With a PML OR a 3" SL, the droop is about the same if the shocks can get to ~ 26" extended.
Adding AAL DOES NOT require longer shocks, as the AAL'd pack is LESS flexible than the stock pack...so a stock pack can require longer shocks than an augmented pack, etc....albeit 16" - 26" range shocks work great for either.
The Bilstein 5100's have a travel range of 16 - 26" (10" of travel), and fit a stock, PML or 3" SL rig, no problem.
They are also valved a bit stiffer than stock though, to help compensate for the added forces when the center of gravity is raised...which is also nice for firming up the control on a stock height rig, especially if its adding some armor, larger tires, etc.
So, all of that means that those Bils for the 3" SL kit are a direct swap for the OEM shocks w/o having to adjust or change anything else....unless you want to take ADVANTAGE of the added potential wheel travel.
This added travel applies to the REAR shocks. The front shocks don't need to be longer, as with the IFS, the arms just go up/down between the bumpstops just like they always do...and even with SLR UCA that add ~ 2" more travel, etc...even the OEM shocks are long enough to allow that.
The front shock replacement will of course sharpen up the ride/handling, and allow a balanced suspension set-up when you change the rears, etc.