If you give your id columns unambiguous names to begin with, things will work
out a lot better for you in the long run.
May I suggest the following modification to your tables to remove ambiguity:
CREATE TABLE x(
x_id INTEGER
);
CREATE TABLE y(
y_id INTEGER,
x_id INTEGER REFERENCES x(x_id)
);
SELECT COALESCE(x_id, y_id) AS id
FROM y
LEFT JOIN x USING (x_id)
GROUP BY id;
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