just took another look at the S3AccessIO.java class. As far as I can see, you won't be able to use different bucket names at the same time, unless you fiddle around with database entries.
The bucketname is part of the storage identifier saved for every dvObject in the database and contains the bucket name. Without having tested this, you should be able to configure a new bucket name for new files and retrieve data from the old bucket unless you are updating the DB records. (IIRC there should be some scripts somewhere in the codebase for these tasks). Be aware that Dataverse expects a certain structure for the keys, which is not explained in detail in the docs AFAIK. (Maybe open an issue for that?)
What are you actually trying to do with the data? If you need the buckets choosable from the UI, that will be tough work. Updating or tampering with this via some clean API would be IMHO easier and cleaner. But it really depends on what you want to achieve...
Maybe you could elaborate a bit more on your use case and maybe open an issue on Github?