has_many :through assoc_ids incorrect with :primary_key option on belongs_to source

Initially reported in the comments at #2421 Problem with has_many :through and alternate keys

Okay, a bit more information. I have:

class Phenotype
  has_many :observations
  has_many :genes, :through => :observations
end

class Observation
  belongs_to :gene, :primary_key => :entrez_id
end

It used to be that when I did Phenotype.find(48291).gene_ids, it would give me the entrez_id attribute rather than the primary keys. This makes sense. I don't use id for anything at all, which is why I set entrez_id as the primary. Unfortunately, in the current beta, gene_ids returns the :id attribute on each gene.

There are obvious workarounds, but this is obnoxious, and it can't be the correct behavior.