The first sentence, (a), doesn't work for my North American dialect.
(a) Mary eats peas, and Bill does so.
so should be "too", or it should come before
does, like this,
(a2) Mary eats peas, and
so does Bill (eat peas).

(a3) Mary eats peas, and Bill does
too (i.e., also).
As for (b), if
so means "also"
, then it's
ungrammatical, but if
does so means "eats peas with honey"; i.e., "does it in that way", then (b) is grammatical.
(b1) I always eat peas with honey, but my wife
never does so/too.

(b2) I always eat peas with honey, but my wife
never does so/does it in that way.