Nearly every diff tool has -w for this, though: main main annoyance with GitHub is that I can’t enable this as the default diff mode.

The indentation rules never change. Fortunately, "SELECT" at six letters is as long as the longest first word that starts a clause, which is why when doing, for example, a "LEFT JOIN" you line up the "LEFT" and not the "JOIN, e.g.

  SELECT a.foo
    FROM alpha a
    JOIN beta b ...

would become

  SELECT a.foo
    FROM alpha a
    LEFT JOIN beta b ...

Any diff tool correctly highlights the only change is the LEFT.