Just had a discussion about this with a cabinet maker friend of mine yesterday.
Like me, he fully inserts the plug first. I always apply a bit of glue and pound 'em in, altho gently.
He uses a flexible Japanese pull saw to cut them flush, after putting a piece of masking tape on each side of the plug. That way he ends up having to sand down one tape-thickness. He swears by this method.
I have used the sharp-chisel method, but there is occasional risk of not reading the side grain on the plug and cutting from the wrong side...
Cheers,
Loren