If you can fit either rack, then think about the future or perhaps other things like fenders.

If you get the non-disc, might you have trouble using that rack on other bikes you buy later if you have a disc unit that is in the way? It is getting harder to find new bikes with rim brakes, who knows what the choices will be in a decade? In part I ask this question because my Tubus Logo has been used on three different touring bikes.

Non-disc - the rack is probably a bit narrower, makes the bike a bit narrower, that can be a minor advantage if traveling. Make sure that this rack will work with the panniers you want and with the disc unit in place. In other words, would the disc brake unit and this rack interfere with the lower hook on a pannier? If so, that might be an issue.

I do not know if you plan to use fenders or not. With the design of the mounts on the Lynskey, if you used the disc version that might allow you to put the rack on the lower mounting point and fender stays on the upper mounting point, lowering the rack slightly.

Those are the issues I would be thinking of if I was in your shoes.