The X-bushing and raising the fork tubes don't change your travel, as long as you do it right and don't let the tire hit the fender, the bike will just bottom out with the tire closer to the fender.
Lowering links are supposed to actually give you more travel, but do soften up the spring rate due to more leverage, and can make linkage bikes handle funky. My old KDX came with a 1" Kouba link and it worked pretty well. I tried a 3" out of my GF's KLX and the handling got super slow, plus the tire hit the fender bad which was compounded by it making the spring way too soft.
Most suspension shops use spacers which does decrease travel, but should't affect the spring rate much.
I guess you could say that the travel of the leg does not change if the leg is not on the bike, but the travel does change as this is what is required to keep enough distance from wheel to fender and what is set at a engineered safe spot.
So anytime you alter travel distance to an item such as a fender than I would say the travel has changed. Even if we do not alter the shock the travel has still changed. We for sure do not want the wheel to hit the fender as it could be catastrophic.
Kouba link requires you to raise the fork legs into the tree to correct rake and trail, X bushing does not as this is a PDS system and all that is moving is the mount, thus bringing the seat down, I strongly suggest against raising the 4CS into the trees, The bike will flop and pain will come shortly after
If one is light then we do not need to worry about compression issues, if sag is set correctly and we have the correct spring. If one is heavy such as I am
, then this can be an issue, but again the 14FE has a ton of clearance. I have been 10 feet in the air and have not compressed tire into fender, however stomach into chin was an issue lmao..
The KlX, If the sag was adjusted after the link was installed the spring rate would not have changed just travel. The only way it would get soft is loss of pressure, settings out of spec, loose spring or wrong spring. The lowering link should not change spring rate just travel. The lowering link give the shock more travel, not the bike, seat still comes down and fender gets closer. I theory this should make the shock stiffer as the link is shorter to give a lower ride.