I have been thoroughly reading through the Alchemist and Inquisitor and though I missed out on biweekly PF Society this week at my local game store I plan on making an Alchemist in the near future.
Now with the way the Society works the Cha Damage won't be a problem as it is resolved at the end of the session (unless there's some post combat Dip checks or the like). But I can see it being a problem in the long term home campaigns where adventures may take place over several days. Rolling a 1 isn't a huge problem since it's gone the next day. Rolling a 4, however, results in a penalty the duration of which means the alchemist isn't using mutagen again for a few days.
With the list of Formulae including things like shield, bull's strength, transformation, true strike, and other such combat effective abilities it definitely seems like a Mr. Hyde/Hulk genetic combat monster is a viable build but the cumulative penalties of doing this measure in days where as the boon is measured in minutes.
I can see the penalty being there for flavor reasons. I can also see it there to keep the Alchemist from doing it every encounter. But making it a potentially twice a week (game time) seems a bit much.
I'm wondering how and why the 1d4 Cha damage was decided as a penalty for something that lasts 10min at level 1. Mechanically it seems out of theme. I would rather it be something more like the fatigue due to Barbarian's Rage.
Mutagens don't seem as potent as Rage to me but the penalties for Mutagens are far magnified. The duration is longer but the Ability & Nat. Armor Bonus is likely only relevant for 1 encounter maybe 2 at higher level depending on spacing. Whereas a Barbarian can turn off a rage at the end of an encounter and use it again for the next one considering he waited around for 2x the 6 seconds in a round he was raging. The fatigue rarely gets in the way of encounters and at worse means the party has to wait around for a bit. Mutagens mean rushing to the next one to ensure the effect is still on and potentially waiting days until the character is reset to it's default.