Can't speak to anything but the warm mod, but he definitely rebuilds the mic and line inputs, not the 1/8 and not the spdif. Not sure if the mic input rebuilds are only when using p48....I'd think not.
Ask Doug, he's very accessible. In any event, you should be able to use the spdif. And I'd guess line in should be fine too. Mic in could be an issue, but I'd bet not if you set it to -18.