Why do you think Alex has trouble with doing Low songs, but is ok with playing a shitload of stuff from The Gathering (DNR, Eyes of Wrath, Riding the Snake, 3 Days in Darkness, in the past also True Believer and I think Down For Life a couple of times too)? Besides they did play Low and Trail of Tears a lot with him back in the band (DFG too, although not recently). Plus remember the Low songs are structured in such a way that there's room for solos (unlike most of TG stuff) where Alex can throw his 5 cents in.
Of course, I'd love to hear Chasing Fear and All I Could Bleed in the setlist, but trust me - they wouldn't do that with any other guitarist in the band either. I think Chuck prefers to do what he considers classics and will rarely agree to mix things up a bit. Alex and, especially, Eric are down for some more experimentation in the setlist, I think.