I suspect that the reason AJ has been through a few Foderas in his time is rooted more in his highly discriminating and/or changing taste rather than any fault with the instruments themselves. Phil Lesh has been through numerous basses over the course of his career-is the fact that he moved away from Alembic the fault of Alembic, or is it because Phil's taste as a player changed?
From reading the article, it seems as though Jackson has remained loyal to Fodera as a result of them being some of, if not the first builders to consider the 6 as a legitimate instrument and their willingness to accommodate his ideas and changing tastes as an artist.
It's impossible to speculate as to whether Alembic would have built him a better instrument-Jackson's current bass, a singlecut with a single pickup wired straight to the jack, is unlike anything in the Alembic line, and it seems unlikely that Alembic would ever build such an instrument.
I'm just glad that we have so many great builders to choose from. Their co-existence is not mutually exclusive, and the great variety of luthiers now practicing their craft means that players are more likely to get a bass that truly suits them, be it from Alembic or from someone else.