I've added in a section in my content repository documents on adding in attributes (extra columns) through this syntax:
select content_type__create_attribute(
'pm_project',
'customer_id',
'integer',
'Customer',
'Customers',
null,
null,
'integer constraint pm_project_customer_fk references organizations'
);
instead of using alter table add column...
Note that by putting the foreign key reference in the column spec (the last argument), I was able to have legitimate foreign key references. I'm not sure if this is supposed to be supported or not, but it works.