I am honestly perplexed by this thread. Whether the guitar player is using a capo, or playing in alternate tuning, whatever does not affect the chord pattern. Finding the key of a song should actually be a "no-brainer" for a bass player. Rarely do I struggle to find the "one" or key of a song. This would especially be true at "jam" sessions that are just that - jamming. In most of my playing situations, I couldn't tell you if the guitarist is using a capo or not. And when I play acoustic rhythm guitar, if the song is in Eb or Bb, rest assured I will use a capo.
I do not mean to sound brash, so forgive me if I do. My suggestion to the OP would be to work on your "key-finding" skills. (is that a word?). Practice at home with songs you are unfamiliar with and work on finding the key they are in. Eventually it will come very easy to almost immediately know what key you are playing in, and also recognize the chord pattern.