Bayesian confirmation theory as a philosophy was originally conceived as a model using only two possibilities

I'm not sure whether this is true, but it's irrelevant. Bayesian confirmation theory works just fine with any number of hypotheses.

then I can't confirm any of them

If by "confirm" you mean "assign high probability to, without further evidence", yes. That seems to me to be exactly what you'd want. What is the problem you see here?