I don't know what you're basing the first statement on. When Boz's "Tour Diary" used to be available on his old website, Alain had been in contact with Boz and Lyn between his departure after Dublin Castle and prior to the UK festival dates in August 2004 then subsequently prior to the U.S. tour in fall 2004. I recall Boz saying he was "raring to go," or something to that effect. Alain had had some combination of personal and health issues that prevented him from continuing the tour - it wasn't from any lack of desire.
And he didn't just write "a few pieces" on Refusal: he wrote five tracks to Boz's and Jesse's three apiece, as well as three contemporary B-sides (if you include "My Dearest Love," which was recorded at the same time) and at least four other unfinished tracks ("Teresa, Teresa," "I'm Looking Forward To Going Back," "When I Was Young," "I Was Bully, Do Not Forget Me"). Per usual, Alain's co-writes comprised the vast majority - essentially, a full album's worth of material in all. To be excluded from performing on that much of one's material had to be more than a bit galling, especially after the the goodwill/faith Your Arsenal, Vauxhall And I and You Are The Quarry alone should have merited.