As stated above, can an Alchemist choose to end the effects of their Mutagen before the total duration has expired? At L14+ (due to Persistent Mutagen) the duration of a Mutagen is 14-20 hours.
No, they cannot.
The mutagen lacks any reference on spells that it works like or how to remove the effect. The only exception being what happens if you drink another mutagen while a previous one is in effect:
Whenever an alchemist drinks a mutagen, the effects of any previous mutagen immediately end.
This ability functions like the beast shape I spell, except as noted here. The effect lasts for 1 hour per druid level, or until she changes back. Changing form (to animal or back) is a standard action and doesn’t provoke an attack of opportunity. The form chosen must be that of an animal the druid is familiar with.
This last part wasn't necessary, as Beast Shape is dismissable, but repeating that information on a core ability of the class might have saved many questions.