MIDI in the BB are commands - small bits of info that tell the BB to do something. For the MIDI parts of the song files, those commands tell the BB to play pre-recorded snippets of drums at a certain time and volume. You can edit those by opening up the midi files for the loops, transitions, and fills associated with a BB song.
For features in the BB, those commands (aka MIDI-IN) tell the BB to start, stop, play fill, play transition etc. The features commands are generated externally to the BB by a midi controller. I just bought some hardware (puc+) and software (midipad) that allow my iPhone to command the BB.
The BB can also generate it’s own commands and control other devices by generating midi commands that align with events going on inside the BB - aka MIDI-OUT. I haven’t used this feature to date but it will allow external devices like loopers to stay in sync with the beat the BB is generating.
None of those commands support transposing pre-recorded tones. You have to ask the developers of those drum kits to provide the pre-recorded sounds in the alternate key or you have to get a (magical but some exist) digital signal processing box to do the transposition for your. The BB does not come with those features.