If you go for an annotated edition you are getting not just Bach but some editor's take on Bach, which is fine as long you are happy to trust him.
With an Urtext edition (e.g. Henle, Barenreiter, ABRSM (?)) you are forced to come to your own interpretation.
I don't think Czerny would pass muster these days. For example, if I remember correctly, he "helpfully" added an extra bar to the C major Prelude of Book one as Bach's harmonic progression was a bit too daring for him.
Having said that, Czerny was a pupil of Beethoven and his annotations of the 48 were informed by Beethoven's teaching, so obviously they are of great historical interest.