I usually go by th Book of Vile Darkness for poisons, drugs, etc.
Reason I could think of why Craft (poisonmaking) exists:
To prevent Craft (alchemy) from becoming to powerful.
Making poisons requires some specialty in handling the toxins that isn't involved in other alchemical procedures.
You might consider synergy bonuses between the two if you feel they should be different yet related, but nothing prevents a DM from merging them.
Perhaps the problem lies more in the generalized thought created by the phrasing of Craft (alchemy).
You could look at it like a General Practitioner compared to a Psychiatrist or something. It's both medicine but the Psychiatrist is much better when dealing with mental issues.
This is supported by some books allowing alchemists to make poisons at higher DCs.