My personal thoughts are that it is preferable to match every item within the fork assembly as closely as possible. The links in particular have faces top & bottom that make contact with the buffers, so they may require an amount of fettling to align.
As for the lower buffers, they surely can only be 'influential' upon the quality of the ride upon rebound. In my experience, that is likely to only be of concern in extremes, such as racing, where heavy braking only occurs prior to a corner, in which case it would be undesirable that they could influence how well the suspension affects the balance of the machine. Done correctly, with braking 'flowing' into the corner & keeping the suspension loaded whilst negotiating the corner, the rebound buffers would not be even touched by the fork links. Otherwise, the lower buffers are only active with the bike on the stand with no load.
Indeed, although I have experimented in the past with cut down lower buffers, there were racers that left them out entirely, but that may have been in conjunction with certain aftermarket dampers that may have obviated the need. (Before anybody gets the wrong idea, I'm not on about BGM etc, although there appear to be many users on this Forum that recommend their use)
As for the top buffers, if they come into play @ all, during extreme hard braking, then the front end will start to bounce, with a rapid series of lock ups/release/lock ups/release that can be quite controllable in a straight line on a dry surface & also an indicator that maximum braking is in operation as far as the suspension & tyres allow. This was a common occurrence when using the Cadwell Club circuit prior to entering the hairpin.
Obviously, in the case of anti-dive, then there may need to be different emphasis upon the roles of the buffers. As far as I am aware, there is no proof that anti-dive is any better than a conventional braking set up, but it appears to sell well, just as whip aerials did, once upon a time. I have known extremely good riders try anti-dive & taken it off, preferring the feel that dive gives them.
I hope this helps
