ALTER TABLE with missing FROM-clause entry for table "inventory" ALTER TABLE inventory.subtitles
   ALTER COLUMN id SET DEFAULT (inventory.subtitle_subtitle_id_seq);

produces missing FROM-clause entry for table "inventory"

but even pgadmin 3 gives me the same syntax.
The problem is in the SET DEFAULT (inventory.subtitle_subtitle_id_seq). Postgres interprets this as "the column subtitle_subtitle_id_seq from the table inventory" which is clearly not your intention.

First of all, you can't get a value from a sequence with just the bare sequence name like that. Generally, you would use nextval('sequence_name').

You probably want something like:

ALTER TABLE inventory.subtitles
    ALTER COLUMN id SET DEFAULT nextval('inventory.subtitle_subtitle_id_seq');