Pepper does not work with the CTAG, both for mechanical reasons (the CTAG's audio I/Os are at the back while the Bela cape's I/Os are at the top), and electrical (none of the outputs of the CTAG gets anywhere close to the 5V we have on the analog outs of the Bela cape).
You could have a CTAG + Bela + Pepper (assuming your Eurorack case is deep enough). You wouldn't be able to use the audio I/O from the Bela cape, but the analog and digital I/O would still work. The audio I/O of the CTAG would be accessible via the header at the back of the board, but would not be broken out to the Eurorack front panel ( unless you jumper two of them across somehow).
Conniemandale My idea is to have the Pepper as a module, but also have the possibility to just remove the Bela from the front panel and create some experiments / installations. What would you recommend.
Then perhaps you could keep the Ctag cape for the "off-rack" use, and the Bela cape for "on-rack" use, sharing the BeagleBone between the two?