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Description
The standard way that the VO-DML tools work is that this model will create a surrogate primary key FKCOLUMN_ID for the key_columns table - this is an extra column compared with the columns defined in the TAP standard - it should be harmless in the sense that queries on this table will usually be making use of the rest of the columns in this table by selecting/Joining on the key_id.
Although the TAP standard is not explicit about whether extra columns are allowed or not, it does allow extra tables in the TAP schema namespace.
An alternative schema design would be to make a composite primary key from the key_id, from_column, target_column columns - the ability to specify this would require changes to VO-DML metadata model as constraints are not allowed for references (to add the desire that the reference should be a primary key - which is probably a strange thing to want normally).
Current tactic with this issue is to wait and see if there is any real world harm from the surrogate primary key.