So I said I'd post a follow up so...
The bombs weren't the problem I thought they would be. It's amazing how you can stress about something, and then have it not be a big deal.
The formula list hasn't been that bad, but have had to tweak it, more for feel than for balance issues.
Player never seemed to want to take feral mutagen, as I was concerned about that one as well.
Even an alchemist can't craft poisons great, it's expensive and the DC's aren't that great. I think some of the bard trade secrets would make good poisoning discoveries. There is one that increases DC of poisons crafted, and another that decreases cost, they might not work in other settings, but I think they are appropriate for DS.
Anyway I think it has worked out fine, if anybody else was thinking about allowing this, I would say to go for it.